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GST Returns for SEZ in Pune: Expert CA-Assisted Filing for SEZ Units & DTA Suppliers

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Reviewed by CA and CS Team, Patron Accounting LLP ICAI & ICSI Registered| 15+ Years Experience| Last Updated: 23 March 2026 Verify Credentials →

SEZ Units: Separate GST registration mandatory; file GSTR-1, GSTR-3B, GSTR-9; supply from SEZ to DTA attracts IGST

DTA Suppliers: Zero-rated supply under Section 16 IGST Act; supply under LUT/Bond or pay IGST and claim refund

Pune SEZ Cluster: 23 operational SEZs with 300+ units; Rs 1 lakh crore+ exports; IT/ITES, pharma, multi-product zones

Refund: DTA suppliers claim ITC refund (LUT route) or IGST refund via Form RFD-01

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Overview What Are SEZ Returns Who Needs Compliance Services Process Documents Challenges Fees Deadlines Why Patron Transaction Matrix FAQs

GST Returns for SEZ in Pune - Overview

📌 TL;DR - GST Returns for SEZ in Pune Services at a Glance

GST returns for Special Economic Zones (SEZ) in Pune involve two distinct compliance streams. SEZ units - the 300+ IT/ITES, pharma, and manufacturing units across 23 Pune SEZs from Hinjewadi to Kharadi - must maintain a separate GST registration and file GSTR-1, GSTR-3B, and GSTR-9. DTA suppliers providing goods or services to Pune SEZ units enjoy zero-rated supply treatment under Section 16 of the IGST Act - they can supply under LUT/Bond without IGST and claim ITC refund, or pay IGST upfront and claim IGST refund via Form RFD-01.

Pune's SEZ ecosystem is among the largest in western India. Qubix Business Park SEZ and MIDC SEZ in Hinjewadi Phase 1 and Phase 3, International Tech Park Pune SEZ in Phase 3, EON Kharadi SEZ, Magarpatta City SEZ, Embassy Tech Zone SEZ in Phase 2, and Serum Bio-Pharma Park SEZ house major IT companies and India's largest vaccine manufacturing facility. The Joint Development Commissioner, Pune Cluster at SEZ Bhawan, Hinjewadi oversees all 23 SEZs. Learn more about GST Returns across India.

In FY 2021-22, Pune's SEZ cluster achieved exports exceeding Rs 1 lakh crore. The CGST Commissionerate Pune-I/II and Maharashtra GST Pune District handle GST compliance while SEZ-specific approvals come from the JDC Pune Cluster. Patron Accounting's Pune office provides end-to-end compliance for both sides. For related services see GST Registration in Pune and GST Returns in Pune. File returns on the GST Portal.

Content is reviewed quarterly for accuracy.

What Are GST Returns for SEZ?

Under GST, Special Economic Zones are treated as territories outside the customs territory of India for supply purposes. Any supply to or by an SEZ unit/developer is classified as an inter-state supply, attracting IGST provisions. SEZ units must obtain a separate GST registration under Section 24 of the CGST Act regardless of turnover. They file regular GSTR-1, GSTR-3B, and GSTR-9.

For DTA suppliers, any supply to an SEZ qualifies as a zero-rated supply under Section 16 of the IGST Act. Two options: supply under LUT/Bond without paying IGST and claim ITC refund, or pay IGST and claim IGST refund through Form RFD-01.

In Pune, where hundreds of DTA businesses supply goods, services and manpower to 23 operational SEZs, understanding this dual framework is essential. Related: GST Refund, GST Audit and GST Notice handling.

Key Terms for GST Returns for SEZ in Pune:

Section 16 IGST Act: Defines zero-rated supply including supply to SEZ unit/developer
GSTR-1 Table 6B: Reporting of supplies to SEZ unit/developer (separate from Table 6A for exports)
LUT (RFD-11): Letter of Undertaking for supply to SEZ without IGST, filed annually
Rule 89(4): Formula for computing ITC refund on zero-rated supply without tax
SEZ Officer Endorsement: Confirmation from JDC Pune Cluster that goods/services were received
DTA Clearance: Sale from SEZ to domestic market - treated as import requiring Bill of Entry + IGST

23 SEZs 300+ Units in Pune

Who Needs SEZ GST Return Compliance in Pune?

SEZ Units in Pune: Over 300 units across 23 SEZs - IT/ITES in Qubix Business Park SEZ (Hinjewadi Phase 1), International Tech Park Pune (Phase 3), EON Kharadi SEZ, and pharma in Serum Bio-Pharma Park SEZ - must file GSTR-1, GSTR-3B, and GSTR-9 under a separate GSTIN.

SEZ Developers: MIDC, Ascendas/CapitaLand, and EON Kharadi Infrastructure must maintain separate registration for developer-specific transactions. Related: GST Registration in Pune.

DTA Suppliers to Pune SEZs: Any registered DTA business supplying goods or services to Pune SEZ units must treat these as zero-rated, report in GSTR-1 Table 6B and claim refund. See also Import Export Code.

Companies with Dual Presence: Infosys, Wipro, KPIT Technologies etc operating both DTA and SEZ units in Pune maintain separate GSTINs for each - inter-entity supplies are distinct taxable transactions.

SEZ GST Return Services in Pune

Service	What We Do
GSTR-1/3B Filing for SEZ Units	Monthly/quarterly outward supply details and summary return with IGST computation for SEZ units. DTA clearances, inter-SEZ supplies and export invoices.
DTA Supplier Zero-Rated Compliance	GSTR-1 Table 6B reporting and LUT/Bond management for DTA businesses supplying to Pune SEZs.
LUT Filing and Renewal (RFD-11)	Annual Letter of Undertaking preparation and filing before April 1 for supply without IGST.
ITC Refund via RFD-01 (LUT Route)	Computing eligible ITC refund under Rule 89(4) for DTA suppliers who supplied to SEZ under LUT.
IGST Refund via RFD-01	Filing refund for DTA suppliers who paid IGST on supply to SEZ. SEZ officer endorsement coordination included.
DTA Clearance + Separate GSTIN	IGST and customs duty computation for SEZ-to-DTA sales. New SEZ unit registration via GST REG-01. Linked with GST Annual Returns and Accounting Services.

Our Process

SEZ GST Return Filing Process in Pune

Our Pune CA team manages the full SEZ GST compliance - SEZ unit returns, DTA supplier zero-rated reporting, LUT management and refund processing.

Step 1

Determine Compliance Stream - SEZ Unit or DTA Supplier

Identify whether your business is an SEZ unit/developer (filing GSTR-1/3B/9 under separate GSTIN) or a DTA supplier (reporting zero-rated supply in Table 6B and claiming refund). For Pune companies with dual DTA-SEZ presence - such as IT firms in both Hinjewadi Phase 1 SEZ and Hinjewadi DTA offices - each entity files independently. Patron maps the full compliance profile across all Pune SEZ locations.

Stream identifiedDual presence mapped

Classified01

Step 2

Obtain/Verify Separate SEZ GSTIN

SEZ units must hold separate GST registration under Section 24 - no threshold exemption. File Form GST REG-01 with SEZ unit/developer option. Registration linked to specific SEZ address (e.g., Qubix Business Park SEZ, Hinjewadi). DTA suppliers ensure existing GSTIN is active and LUT valid. CGST Commissionerate Pune-I/II processes registrations.

SEZ GSTIN obtainedRegistration verified

Registered02

Step 3

File LUT for Zero-Rated Supply (DTA Suppliers)

DTA suppliers file Form GST RFD-11 annually on the GST portal before April 1. LUT allows supply to Pune SEZ units without payment of IGST, improving cash flow significantly. Once accepted, covers all supplies to any Pune SEZ during the year. Patron files LUT renewals for all DTA supplier clients before the deadline.

LUT filed (RFD-11)Annual renewal tracked

LUT Active03

Step 4

Report SEZ Supplies in GSTR-1

SEZ units: DTA clearances in Table 4A, inter-SEZ supplies, exports in Table 6A. DTA suppliers: zero-rated supplies in Table 6B with SEZ unit's GSTIN, invoice details, taxable value and IGST amount (or 'without payment of tax' under LUT). Obtain endorsement from SEZ officer at JDC Pune Cluster confirming receipt.

Table 6B reportedEndorsement obtained

GSTR-1 Filed04

Step 5

File GSTR-3B with Correct SEZ Treatment

SEZ units: output tax on DTA clearances in Table 3.1(a), ITC in Table 4. DTA suppliers (LUT): zero-rated in Table 3.1(b). DTA suppliers (IGST paid): Table 3.1(b) with IGST payment through electronic ledger - refundable via RFD-01. Patron cross-verifies all figures before filing.

GSTR-3B filedSEZ treatment correct

3B Complete05

Step 6

Claim Refund via RFD-01 (DTA Suppliers)

Navigate to Services > Refunds on gst.gov.in. Select 'supplies to SEZ with/without payment of tax'. Upload offline utility with invoice-wise details matching GSTR-1. Ensure SEZ officer endorsement is obtained from JDC Pune Cluster. Refund computed under Rule 89(4) for LUT route. Processing within 30-60 days. Patron manages the entire cycle.

RFD-01 filedRefund processed (30-60 days)

Refund Received06

Documents Required for SEZ GST Compliance in Pune

SEZ Unit Registration Certificate: Letter of Approval (Form B/C/B1) from Development Commissioner.
Separate GSTIN Certificate: GST registration under SEZ unit/developer category.
LUT (Form GST RFD-11): Annual Letter of Undertaking for DTA suppliers opting zero-rated without IGST.
Tax Invoice with SEZ Declaration: "Supply meant for SEZ Unit/Developer under LUT/Bond without payment of tax".
Bill of Export: For goods supplied from DTA to SEZ (deemed export).
SEZ Officer Endorsement: Confirmation from JDC Pune Cluster of receipt of goods/services.
Delivery Challan / Transport Documents: For goods movement with e-way bill for value > Rs 50,000.
ITC Register: For DTA suppliers claiming ITC refund under Rule 89(4).

Pune-specific tip: For DTA suppliers serving multiple Pune SEZs (e.g., both Qubix SEZ in Hinjewadi and EON Kharadi SEZ), maintain separate invoice series or tracking for each SEZ unit GSTIN to simplify GSTR-1 Table 6B reporting and RFD-01 refund computation.

Common SEZ GST Compliance Challenges in Pune

Challenge	Impact	How Patron Accounting Solves It
Separate Registration Confusion	Companies opening in Pune SEZ fail to obtain separate GSTIN before commencing operations under Section 24	Patron obtains SEZ GSTIN proactively as part of onboarding for every SEZ client
GSTR-1 Table 6B Errors	DTA suppliers report with DTA GSTIN instead of SEZ unit GSTIN - refund rejected	Patron verifies SEZ unit GSTIN for every Table 6B entry before filing
SEZ Officer Endorsement Delays	JDC Pune Cluster endorsement delays hold up entire refund cycle	Patron coordinates directly with JDC office at SEZ Bhawan Hinjewadi to expedite
LUT Expiry and Non-Renewal	DTA suppliers miss April 1 renewal - forced to pay IGST increasing working capital needs	Patron maintains LUT renewal calendar and files before deadline for all SEZ clients

SEZ GST Return Filing Fees in Pune

Fee Component	Amount
GSTR-1/3B Monthly (SEZ unit)	Patron Rs 5,000-15,000/month (incl. DTA clearance)
GSTR-9 Annual (SEZ unit)	Patron Rs 10,000-25,000/year
DTA Supplier Returns (GSTR-1/3B)	Patron Rs 3,000-10,000/month (Table 6B reporting)
LUT Filing / Renewal (RFD-11)	Patron Rs 3,000-7,000/year
ITC Refund via RFD-01 (LUT route)	Patron Rs 7,000-25,000/claim
IGST Refund via RFD-01	Patron Rs 7,000-20,000/claim
Separate SEZ GSTIN Registration	Patron Rs 5,000-12,000 (one-time)
SEZ Officer Endorsement Coordination	Patron Rs 3,000-8,000/quarter

All fees and charges listed are indicative only and do not constitute a binding offer. Final amounts may vary depending on the volume of work and the complexity involved.

Professional service charges for drafting, filing, and representation are separate from the statutory fees. The exact fee depends on the complexity of the case, disputed amount, and number of hearings required. Contact us for a detailed quote.

Get a free GST Returns for SEZ in Pune consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

SEZ GST Return Filing Deadlines

Stage	Estimated Timeline
GSTR-1 (monthly)	11th of the following month
GSTR-1 (quarterly - QRMP)	13th of month following quarter
GSTR-3B (monthly)	20th of the following month
GSTR-9 (annual)	31st December of following FY
LUT Renewal (RFD-11)	Before April 1 each year
RFD-01 (Refund)	Within 2 years from relevant date
Bill of Export	At the time of supply to SEZ

Pune Processing Note: SEZ officer endorsement is obtained from the JDC Pune Cluster at SEZ Bhawan, Plot No. 6/1, MIDC, Phase-III, Hinjewadi, Pune 411057. Patron coordinates endorsement directly. All GST returns filed online via gst.gov.in. Refunds processed within 30-60 days with complete documentation.

Key Benefits

Why Choose Patron for SEZ GST Returns in Pune?

Pune Office + 23 SEZ Coverage

RTC Silver, Wagholi - serving all 23 Pune SEZs including Hinjewadi Phase 1/2/3, EON Kharadi, Magarpatta City, Serum Bio-Pharma Park and Khed.

Dual SEZ Compliance

Both SEZ unit returns (GSTR-1/3B/9) and DTA supplier compliance (Table 6B, LUT, RFD-01 refund) from a single service point.

JDC Pune Liaison

Direct coordination with Joint Development Commissioner, Pune Cluster at SEZ Bhawan for endorsements, clearances and compliance queries.

30-60 Day Refund Processing

Complete RFD-01 cycle from Rule 89(4) computation to offline utility upload, endorsement coordination and refund tracking.

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"Our GST filing is always on time since we moved to Patron. The CA team knows their stuff cold." - CFO, Manufacturing, Maharashtra

With offices in Pune, Mumbai, Delhi and Gurugram, Patron serves SEZ units, IT companies and DTA suppliers across India.

SEZ GST Transaction Matrix

Transaction	GST Treatment	Who Pays
DTA to SEZ (LUT)	Zero-rated	No IGST; ITC refund via RFD-01
DTA to SEZ (IGST)	Zero-rated	DTA supplier pays IGST; IGST refund via RFD-01
SEZ to DTA	Import into India	SEZ unit/DTA buyer (IGST + BCD via Bill of Entry)
SEZ to Export	Export (zero-rated)	No tax paid; GSTR-1 Table 6A
Inter-SEZ (same/different)	Zero-rated	No GST; reported in GSTR-1
Import into SEZ	Exempt (NN 18/2017-IT)	No IGST
Services imported by SEZ	Exempt (NN 18/2017-IT(R))	No RCM required

Related Services

For Pune businesses needing related GST and SEZ compliance services:

Legal and Compliance Framework for SEZ GST

Section 16, IGST Act 2017: Zero-rated supply includes supply to SEZ unit/developer. Two options: LUT/Bond (no IGST) or pay IGST and claim refund.

Section 24, CGST Act 2017: Mandatory separate GST registration for SEZ units/developers. No threshold exemption.

Section 7(5)(b), IGST Act: Supply to/by SEZ treated as inter-state supply. IGST applicable.

Rule 89(4): Formula for ITC refund on zero-rated supply without tax payment.

Notification No. 18/2017-IT: Exempts goods imported into SEZ from IGST. Services imported by SEZ for authorised operations also exempt.

Form GST RFD-11: LUT for supply without IGST. Annual filing, valid one financial year.

Form RFD-01: Refund application for DTA suppliers (with or without tax payment).

GSTR-1 Table 6B: Reporting of supplies to SEZ (separate from Table 6A exports).

Portal: gst.gov.in

SEZ Authority: JDC Pune Cluster, SEZ Bhawan, Plot 6/1, MIDC Phase-III, Hinjewadi, Pune 411057 (under Zonal DC, SEEPZ-SEZ, Mumbai).

GST Authority: CGST Commissionerate Pune-I/II (punecgstcus.gov.in). Maharashtra GST Pune District (mahagst.gov.in).

FAQs - GST Returns for SEZ in Pune

Find answers to the most common questions about SEZ GST compliance in Pune.

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Which GST office handles SEZ compliance in Pune?

The CGST Commissionerate Pune-I and Pune-II handle GST registration and return compliance for SEZ units and DTA suppliers. The Joint Development Commissioner, Pune Cluster at SEZ Bhawan, Hinjewadi oversees SEZ-specific approvals, endorsements and operational compliance for all 23 Pune SEZs. Patron manages all filings from its Pune office.

Is supply to SEZ zero-rated under GST?

Yes. Under Section 16 of the IGST Act, 2017, any supply of goods or services to an SEZ unit or developer is a zero-rated supply. DTA suppliers can supply under LUT/Bond without paying IGST and claim ITC refund, or pay IGST upfront and claim IGST refund. Both options result in effective zero GST. The LUT route is preferred for better cash flow.

Which SEZs operate in Pune?

Pune has 23 operational SEZs with over 300 units, primarily in IT/ITES and pharmaceuticals. Major SEZs include Qubix Business Park SEZ (Hinjewadi Phase 1), International Tech Park Pune (Phase 3), EON Kharadi SEZ, Magarpatta City SEZ, Embassy Tech Zone SEZ (Phase 2), MIDC SEZ (Phase 3), Serum Bio-Pharma Park SEZ, and Khed Economic Infrastructure SEZ.

Do SEZ units need separate GST registration?

Yes. Under Section 24 of the CGST Act, SEZ units and developers must obtain a separate GST registration irrespective of turnover. A company with a DTA office in Baner, Pune and an SEZ unit in Hinjewadi Phase 1 must hold two separate GSTINs - both in Maharashtra, but treated as distinct persons. Inter-entity supplies are taxable.

How do DTA suppliers claim refund on supply to Pune SEZ?

File Form RFD-01 on the GST portal. For LUT route: select 'supplies to SEZ without payment of tax' with invoice-wise details matching GSTR-1 Table 6B, computed under Rule 89(4). For IGST route: select 'with payment of tax'. Both require SEZ officer endorsement from JDC Pune Cluster. Refunds typically processed within 30-60 days.

What happens when an SEZ unit sells to DTA?

When a Pune SEZ unit sells to the domestic market, it is treated as an import into India. The SEZ unit or DTA buyer must file a Bill of Entry, pay Basic Customs Duty + Social Welfare Surcharge + IGST at applicable rates, and clear through customs. The IGST paid is available as ITC to the DTA buyer.

Are services imported by Pune SEZ units exempt from GST?

Yes. Under Notification No. 18/2017-Integrated Tax (Rate), services imported by an SEZ unit or developer for authorised operations are exempt from GST. No reverse charge applies. This covers services from outside India consumed within the Pune SEZ for authorised business activities.

What is GSTR-1 Table 6B for SEZ?

Table 6B in GSTR-1 is specifically for reporting supplies to SEZ unit or developer - distinct from Table 6A which covers exports. DTA suppliers must report the SEZ unit's GSTIN (not DTA GSTIN), invoice details, taxable value and IGST amount or mark as 'without payment of tax' under LUT.

Quick Answers

SEZ ka zero-rated supply kya hai? Section 16 IGST Act ke under SEZ unit/developer ko supply - zero GST lagta hai. LUT se without IGST supply karo aur ITC refund lo, ya IGST pay karo aur refund RFD-01 se lo.

Pune mein SEZ ka GST return kaise file karein? SEZ unit: Alag GSTIN lein, GSTR-1/3B/9 file karein. DTA supplier: Table 6B mein zero-rated report karein, LUT file karein, RFD-01 se refund lein.

Pune mein kitne SEZ hain? 23 operational SEZs with 300+ units. JDC Pune Cluster at SEZ Bhawan, Hinjewadi. IT/ITES, pharma and multi-product zones.

Don't Miss Your LUT Renewal or Refund Window

GSTR-1 is due by the 11th and GSTR-3B by the 20th every month for SEZ units. LUT must be renewed before April 1 each year - failing which DTA suppliers lose zero-rated benefit. Refund claims under RFD-01 have a 2-year limitation. The CGST Commissionerate Pune and JDC Pune Cluster are actively monitoring compliance. With Pune's SEZ cluster generating Rs 1 lakh crore+ in exports, even minor return errors trigger audit notices and refund rejections.

Get SEZ GST compliant now - Call +91 945 945 6700 or WhatsApp us. Free compliance assessment.

Get Your SEZ GST Compliance Right in Pune

GST returns for SEZ in Pune involve a specialised compliance framework spanning SEZ unit return filing, DTA supplier zero-rated reporting, LUT management and refund processing. With 23 operational SEZs, 300+ units and exports exceeding Rs 1 lakh crore, Pune's SEZ landscape demands precision in every aspect of GST compliance.

Patron Accounting's Pune office at RTC Silver, Wagholi provides end-to-end SEZ GST services covering both sides - SEZ unit returns and DTA supplier refund management - with direct JDC Pune Cluster liaison.

With 15+ years experience, 10,000+ businesses served and a 4.9 Google rating, Patron serves SEZ units and DTA suppliers across Pune, Mumbai, Delhi and Gurugram.

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Content Created: 23 March 2026 | Last Updated: 23 March 2026 | Next Review: 23 September 2026 | Reviewed By: CA & CS Team, Patron Accounting LLP

This page is reviewed semi-annually to reflect SEZ GST rule changes, refund formula updates and JDC Pune Cluster procedural changes. Last review: March 2026. Next review: September 2026.