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GST Returns for SEZ in Mumbai: Zero-Rated Compliance for Units, Developers, and DTA Suppliers

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Supply to SEZ: Zero-rated under Section 16 IGST Act. LUT route (no IGST, claim ITC refund) or IGST payment route (pay upfront, claim IGST refund)

SEZ Unit: Separate GSTIN as SEZ unit/developer. GSTR-1 + GSTR-3B monthly. Service imports exempt for authorised operations

DTA Supplier: GSTR-1 Table 6A for SEZ supply + GSTR-3B + RFD-01 refund claim. 90% provisional refund within 7 days (Rule 91)

Mumbai SEZs: SEEPZ (Andheri East), IT/ITeS SEZs (Airoli, Mahape, Goregaon), Navi Mumbai SEZ, JNPT FTWZ

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Overview What Are Returns Who Files Services Process Documents Challenges Fees Timeline Why Patron LUT vs IGST FAQs

SEZ GST Returns in Mumbai: Complete Overview

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

Supply to SEZ = zero-rated (Section 16 IGST). LUT route (no IGST, ITC refund) or IGST route (pay upfront, IGST refund). SEZ units file GSTR-1/3B with separate SEZ GSTIN. DTA suppliers report in Table 6A + claim refund via RFD-01. 90% provisional in 7 days. SEEPZ (since 1973), IT SEZs Airoli/Mahape, Navi Mumbai SEZ, JNPT FTWZ. Dev Commissioner endorsement required.

Mumbai hosts India's oldest and most prominent SEZs - SEEPZ at Andheri East (since 1973), IT/ITeS SEZs at Airoli, Mahape, Goregaon, Navi Mumbai SEZ mega project, and JNPT Free Trade Warehousing Zone.

Parameter	Detail
Supply TO SEZ	Zero-rated (S.16 IGST). LUT route or IGST + refund route
Supply BY SEZ to DTA	Import by DTA. Customs duty payable by recipient
SEZ Unit Returns	GSTR-1 + GSTR-3B with separate SEZ GSTIN (S.24 mandatory)
DTA Supplier Returns	GSTR-1 Table 6A + GSTR-3B + RFD-01 refund
Service Import (SEZ)	Exempt for authorised ops (Notification 18/2017)
Refund	90% provisional in 7 days (Rule 91). Final 60 days
Dev Commissioner	Endorsement required for refund claims

Patron handles both SEZ unit and DTA supplier compliance from Marine Lines. Related: GST returns, GST refund, GST registration, IEC, GST audit.

Content is reviewed quarterly for accuracy.

What Are GST Returns for SEZ?

GST returns for SEZ cover the unique tax treatment of Special Economic Zones under the IGST Act, 2017 - where supplies to SEZ are zero-rated and supplies by SEZ to DTA are treated as imports, creating distinct return obligations for both SEZ units and their DTA suppliers.

DTA supplier: report zero-rated supply in GSTR-1 Table 6A, claim refund via RFD-01 (LUT or IGST route). SEZ unit: file GSTR-1/3B with separate GSTIN, ITC on DTA inputs, service import exemption for authorised operations.

Filed on gst.gov.in. Dev Commissioner endorsement from SEEPZ/other SEZ. GST returns national. GST refund.

Key Terms for SEZ GST Returns:

Zero-Rated (S.16 IGST): Supply to SEZ = no GST. DTA supplier uses LUT (no IGST, ITC refund) or pays IGST (IGST refund). Both via RFD-01.
LUT (RFD-11): Letter of Undertaking filed annually before first supply. Avoids IGST payment. ITC refund claimed later. Preferred for Mumbai DTA suppliers.
SEZ GSTIN: Separate registration under S.24 CGST. LOA from Dev Commissioner uploaded. Independent GSTR-1/3B filing from normal GSTIN.
Authorised Operations: Dev Commissioner-endorsed activities. Service imports exempt (Notification 18/2017). Non-authorised = IGST RCM payable.
SEEPZ: Santacruz Electronic Export Processing Zone, Andheri East. India's oldest EPZ (1973). Electronics, gems, jewellery, IT. Dev Commissioner on-site.
SEZ-to-DTA: Treated as import by DTA recipient. Customs duty payable. SEZ reports outward in GSTR-1. Not zero-rated in reverse direction.

SEZ Filed

Who Files SEZ GST Returns in Mumbai?

SEEPZ Units (Andheri East): Electronics, gems, jewellery, IT. Separate SEZ GSTIN. GSTR-1/3B monthly. Service import exemption for authorised ops. GST registration.

IT/ITeS SEZ Units (Airoli, Mahape, Goregaon): Software, BPO exports. Table 6A for export services. ITC on domestic inputs refunded. Import Export Code.

DTA Suppliers to SEZ: Andheri MIDC, Powai, BKC businesses supplying goods/services to SEZ. GSTR-1 Table 6A + RFD-01 refund. LUT preferred. GST refund.

Navi Mumbai SEZ + JNPT FTWZ: Multi-product units, warehousing. Fresh registration, GSTR-1/3B from first month. Schedule III for FTWZ goods. GST audit.

SEZ Developers + Dual-GSTIN Entities: Infrastructure developers file with SEZ GSTIN. Companies with both DTA and SEZ operations file independently for each. Statutory audit.

SEZ GST Return Services

Service	What We Do
SEZ Unit GSTR-1/3B Filing	Monthly filing with SEZ GSTIN. Exports Table 6A, DTA clearances, inter-SEZ. ITC on DTA inputs. For SEEPZ and IT SEZ units with high-volume export invoices and HSN-level detail
DTA Supplier Zero-Rated Reporting	GSTR-1 Table 6A for supply to SEZ: SEZ unit GSTIN, invoice details, LUT/bond reference or IGST. Consistency with refund application data ensured
LUT Filing and Management	Annual Form RFD-11 before first supply of FY. Patron files by 31 March for all DTA supplier clients. Ensures uninterrupted zero-rated supply from Day 1
ITC/IGST Refund (RFD-01)	Full refund lifecycle: Statement 4 (IGST route) or ITC computation (LUT route). Portal filing, deficiency response, disbursement tracking. 90% provisional in 7 days
Service Import Exemption	For SEZ units: ensuring Notification 18/2017 exemption correctly applied for authorised operations. No RCM on exempt imports. Non-authorised = IGST RCM computed and reported
Dev Commissioner Coordination	Endorsement for authorised operations and refund claims. SEEPZ and other Mumbai SEZ office coordination. Early engagement for timely processing
SEZ Registration	Fresh SEZ unit/developer GSTIN on GST portal. LOA upload. Reason code selection. Separate from existing normal taxpayer GSTIN
E-Way Bill for SEZ Supply	Mandatory for goods to/from SEZ (inter-state treatment) if value exceeds Rs 50,000. Even for Andheri MIDC to SEEPZ within same area

Our Process

SEZ GST Return Filing Process in Mumbai

Our 6-step process covers complete SEZ GST compliance from perspective determination through GSTIN registration, supply route selection, GSTR-1/3B filing, to RFD-01 refund claim.

Step 1

Determine Filing Perspective

Identify SEZ unit/developer (own GSTR-1/3B with SEZ GSTIN) or DTA supplier (zero-rated reporting + refund). For Mumbai entities with both (Andheri normal + SEEPZ SEZ), both GSTINs need separate filings. Patron Marine Lines assesses complete scope.

Perspective identifiedBoth GSTINs mappedDual filing scoped

Classified 01

Step 2

Register/Verify SEZ GSTIN

SEZ units: register separately as SEZ Unit/Developer on GST portal. Upload LOA from Development Commissioner. DTA suppliers: verify SEZ unit GSTIN is active and correctly classified. For new SEEPZ or Navi Mumbai SEZ units, Patron handles fresh registration.

SEZ GSTIN registeredLOA uploadedActive status verified

Registered 02

Step 3

Choose Supply Route (DTA Supplier)

LUT Route: file RFD-11 before first supply. Supply without IGST. Claim ITC refund later. IGST Route: supply with IGST, claim IGST refund. LUT preferred for Mumbai DTA suppliers - avoids working capital blockage. Patron files LUT annually before 31 March.

Route selectedLUT filed if chosenWorking capital optimised

Route Set 03

Step 4

File GSTR-1 with SEZ Supply Details

DTA suppliers: Table 6A with SEZ unit GSTIN, invoice details, LUT reference or IGST. SEZ units: outward supplies (exports Table 6A, DTA clearances, inter-SEZ). File by 11th monthly or 13th QRMP. Patron files by 8th.

Table 6A populatedSEZ GSTIN referencedFiled by 8th

GSTR-1 Filed 04

Step 5

File GSTR-3B with ITC/IGST

DTA suppliers: zero-rated outward, ITC on inputs (LUT route) or IGST paid (IGST route). SEZ units: outward liability on DTA/domestic, ITC on DTA inputs, RCM on non-authorised services. File by 20th. Patron files by 17th.

Zero-rated reportedITC claimedFiled by 17th

GSTR-3B Filed 05

Step 6

File RFD-01 Refund (DTA Suppliers)

After GSTR-1/3B filed: Services > Refunds > Application for Refund. Select SEZ supply with/without payment. Upload Statement 4 or ITC computation. Dev Commissioner endorsement attached. 90% provisional in 7 days (Rule 91). Final in 60 days.

RFD-01 filedDev Commissioner endorsed90% in 7 days

Refunded 06

Documents Required for SEZ GST Filing

SEZ GSTIN Certificate: With LOA from Development Commissioner for SEZ units.
Tax Invoices: DTA to SEZ with SEZ GSTIN, LUT reference or IGST. SEZ outward: export invoices, DTA clearance invoices.
LUT (Form RFD-11): Valid for FY, filed before first supply. For DTA suppliers on LUT route.
SEZ Endorsement: Dev Commissioner confirmation of goods/services received for authorised operations. Required for refund.
RFD-01 Supporting: Statement 4 (IGST route) or ITC computation (LUT route). CA certificate if required.
E-Way Bill: For goods to/from SEZ (inter-state treatment, value > Rs 50,000).
Import Docs (SEZ Unit): Bills of Entry for goods imported into SEZ.

Mumbai Tip: DTA suppliers at Andheri MIDC supplying to SEEPZ (both Andheri East) must treat supply as inter-state despite physical proximity. IGST applies, not CGST+SGST. E-way bill mandatory if value > Rs 50,000. Dev Commissioner endorsement from SEEPZ required for refund. Patron coordinates the endorsement process.

Common SEZ GST Challenges in Mumbai

Challenge	Impact	How Patron Accounting Solves It
LUT vs IGST Working Capital	IGST route blocks working capital until refund (60 days to 6 months). Missing LUT filing forces IGST on all SEZ supplies until LUT in place	LUT filed annually before 31 March. Uninterrupted zero-rated supply from Day 1. ITC refund managed separately. No working capital blockage
Dev Commissioner Delays	Endorsement for authorised operations can vary in processing time at SEEPZ. Delays block refund claims. Time-sensitive for large-value suppliers	Early coordination with Dev Commissioner office. Endorsement process initiated before refund filing window. Patron manages SEEPZ liaison
Authorised vs Non-Authorised Ops	Misclassification: exempt service imports charged RCM (blocked capital) or non-exempt services not charged (demand exposure). LOA interpretation ambiguous	LOA analysed against each service import. Authorised ops correctly exempted. Non-authorised IGST RCM computed and reported. Clear documentation maintained
Inter-SEZ Transfer Docs	SEEPZ to Navi Mumbai SEZ: inter-state supply. Both GSTINs must reflect. Missing documentation on either side = reconciliation mismatch	Both SEZ GSTINs coordinated. Inter-state IGST correctly applied. Mirror documentation on both sides. E-way bill generated
FTWZ Classification at JNPT	Supply of warehoused goods before clearance may fall under Schedule III. Classification uncertainty affects returns and ITC	FTWZ transaction analysis per Schedule III Entry 8(a). Correct return disclosure. ITC treatment clarified. Expert guidance for JNPT FTWZ clients

SEZ GST Filing Fees

Fee Component	Amount
GST Filing (Govt)	Nil
Late Fee (GSTR-1/3B)	Rs 50+50/day (max Rs 5,000+5,000)
RFD-01 Filing (Govt)	Nil
Patron: SEZ Unit Filing	Starting Rs 3,000/month
Patron: DTA Supplier Compliance	Starting Rs 5,000/month
Patron: LUT Filing	Starting Rs 2,000/year
Patron: RFD-01 Refund	Starting Rs 5,000/claim

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 SEZ GST Returns consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

SEZ GST Filing Timeline

Stage	Estimated Timeline
LUT Filing (RFD-11)	Before first supply of FY
GSTR-1 (Monthly)	11th of following month
GSTR-3B (Monthly)	20th of following month
RFD-01 Refund	Within 2 years of relevant date
90% Provisional Refund	Within 7 days of acknowledgment
Final Refund Order	Within 60 days

Note: DTA suppliers must file LUT before first supply each FY - missing this means IGST on all SEZ supplies. Refund deadline is 2 years absolute. SEZ units must file GSTR-1/3B monthly - non-filing = late fees + GSTIN suspension disrupting SEZ operations. Patron files LUT by 31 March, GSTR-1 by 8th, GSTR-3B by 17th.

Key Benefits

Why Choose Patron for SEZ GST in Mumbai

Dual-Perspective Expertise

Manages both SEZ units (SEZ GSTIN filing) and DTA suppliers (zero-rated reporting + refund). Both sides correctly reported. No cross-referencing mismatches during audit.

Dev Commissioner Coordination

Experience with SEEPZ Development Commissioner and other Mumbai SEZ authorities. Authorised operation endorsements coordinated for timely refund claims and service import exemptions.

Refund Track Record

End-to-end RFD-01 for DTA-to-SEZ. LUT filing, Statement 4, portal filing, deficiency response, disbursement tracking. 90% provisional within 7-day statutory timeline.

Mumbai SEZ Coverage

SEEPZ, IT SEZs Airoli/Mahape/Goregaon, Navi Mumbai SEZ, JNPT FTWZ. 10,000+ businesses, 4.9 rating, 15+ years, 4 offices.

Trusted by SEZ Units and Suppliers Across Mumbai

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Offices in Pune, Mumbai, Delhi, and Gurugram. SEZ/export GST expertise. Dual-perspective compliance for units and DTA suppliers.

LUT Route vs IGST Payment Route

Factor	LUT Route (Without IGST)	IGST Payment Route
IGST Payment	No IGST paid at supply	IGST paid upfront
Working Capital	No blockage - preferred	Blocked until refund processed
Refund Type	ITC refund via RFD-01	IGST refund via RFD-01
Processing	60 days statutory	60 days statutory
LUT Required	Yes - RFD-11 before first supply	No LUT needed
Best For	Most Mumbai DTA suppliers	Suppliers unable to file LUT

Related Services

Mumbai SEZ units and DTA suppliers often need:

GST Returns - General filing guide.
GST Refund - RFD-01 refund claims.
GST Registration in Mumbai - New/SEZ registration.
Import Export Code - For exporters.
GST Audit - Department audit support.
Statutory Audit - Annual audit.

Legal Framework for SEZ GST

IGST Act, 2017:

S.16(1)(b): Supply to SEZ = zero-rated. S.16(3): LUT route or IGST + refund route. S.24 CGST: Compulsory separate registration.

Rules and Notifications:

Rule 89: RFD-01 refund. Rule 91: 90% provisional in 7 days. Notification 18/2017: Service import exemption for authorised ops.

SEZ Act, 2005:

Development Commissioner: endorses authorised operations. LOA: Letter of Approval for SEZ unit operations.

Mumbai SEZs: SEEPZ, IT SEZs, Navi Mumbai SEZ, JNPT FTWZ. GST Portal

FAQs: SEZ GST Returns in Mumbai

Get answers about SEZ GST office, SEZ unit GST liability, separate registration, DTA refund process, LUT vs IGST, service import exemption, SEZ returns, and dual GSTIN.

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Which GST office handles SEZ returns in Mumbai?

SEZ units file returns online at gst.gov.in using their SEZ-specific GSTIN. The jurisdictional GST Commissionerate East West Central or South handles scrutiny based on the SEZ registered address. SEEPZ units fall under Mumbai East jurisdiction. DTA suppliers file under their own jurisdictional zone. The Development Commissioner handles authorised operation approvals. Patron Marine Lines office manages both SEZ units and DTA suppliers.

Do SEZ units pay GST?

SEZ units do not pay GST on supplies received from DTA for authorised operations as these are zero-rated. They do not pay RCM on service imports for authorised operations under Notification 18/2017. However SEZ units must charge and pay GST on supplies made to DTA treated as inter-state supply. DTA recipients treat SEZ-to-DTA supply as import and pay customs duty.

Is separate GST registration required for SEZ?

Yes under Section 24 of the CGST Act SEZ units and developers must register separately on the GST portal with a dedicated SEZ GSTIN. This is distinct from any normal taxpayer GSTIN. The registration requires selection of SEZ Unit or SEZ Developer as reason and upload of LOA from the Development Commissioner.

What is the refund process for DTA suppliers to Mumbai SEZ?

DTA suppliers claim refund through Form RFD-01 after filing GSTR-1 and GSTR-3B. Select supply to SEZ with or without payment of tax. Upload Statement 4 or ITC computation. Development Commissioner endorsement required. 90 percent provisional refund within 7 days under Rule 91. Final order within 60 days.

What is the difference between LUT route and IGST route?

LUT route means DTA supplier supplies without paying IGST under Letter of Undertaking Form RFD-11 and claims ITC refund later. No working capital blockage. IGST route means supplier pays IGST upfront and claims IGST refund. Working capital blocked until processed. Both available under Section 16(3) IGST Act. LUT route preferred for Mumbai suppliers.

Are service imports by SEZ exempt from GST?

Yes for authorised operations only under Notification 18/2017. SEZ unit does not pay RCM on these services. However services imported for non-authorised operations are not exempt and attract IGST under RCM payable and reported in the SEZ unit GSTR-3B. Development Commissioner LOA specifies authorised operations.

What returns do SEZ units file?

SEZ units file GSTR-1 monthly by 11th and GSTR-3B by 20th using their SEZ GSTIN. GSTR-9 annual return if turnover exceeds Rs 2 crore by 31 December. QRMP scheme available for turnover up to Rs 5 crore. Nil returns mandatory even for months with no transactions.

Can a Mumbai company have both normal and SEZ GSTIN?

Yes a company with a manufacturing unit in Andheri DTA and an export unit in SEEPZ SEZ will have two separate GSTINs. Each requires independent GSTR-1 and GSTR-3B filing. Supply between the DTA unit and SEZ unit of the same company is treated as zero-rated inter-state supply.

Quick Answers

SEZ ko supply karne pe GST lagta hai kya? Nahi. Zero-rated hai Section 16 IGST ke under. LUT se supply karo (bina IGST) ya IGST pay karke refund lo.

SEZ unit ko alag registration chahiye? Haan. Section 24 ke under mandatory separate GSTIN. LOA upload karna padta hai.

SEZ unit kaunse returns file karta hai? GSTR-1 (11th) + GSTR-3B (20th) monthly. Apne SEZ GSTIN se. Normal GSTIN se alag.

File LUT Before First Supply - Every Year

DTA suppliers: missing LUT = IGST on all SEZ supplies, blocking working capital. Refund claims must be filed within 2 years - miss it and forfeit permanently. SEZ units: non-filing = late fees + GSTIN suspension disrupting SEZ operations. Dev Commissioner endorsement delays can block refund claims. Mumbai hosts SEEPZ, IT SEZs, Navi Mumbai SEZ, JNPT FTWZ - among the highest DTA-SEZ transaction volumes in India.

Get started - Call +91 945 945 6700 or WhatsApp us.

Zero-Rated Done Right - Both Sides of the SEZ Transaction

SEZ GST in Mumbai covers dual compliance: SEZ units filing with SEZ GSTIN and DTA suppliers reporting zero-rated supplies and claiming refunds. SEEPZ, IT SEZs, Navi Mumbai SEZ, JNPT FTWZ generate complex transactions requiring precise filing.

LUT route preferred for Mumbai DTA suppliers - no working capital blockage. 90% provisional refund in 7 days. Dev Commissioner endorsement coordinated. Service import exemption for authorised operations correctly applied.

Patron provides dual-perspective filing, LUT management, RFD-01 refund lifecycle, Dev Commissioner coordination, and multi-GSTIN management from Marine Lines. 10,000+ businesses, 4.9 rating, 15+ years.

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Content Created: 24 March 2026 | Last Updated: 24 March 2026 | Next Review: 24 June 2026 | Reviewed By: CA & CS Team, Patron Accounting LLP

This page covers GST returns for SEZ in Mumbai. Content reviewed quarterly (Freshness Tier 1) as SEZ provisions, notifications, and Development Commissioner requirements evolve.