Payroll Services for Healthcare Companies in India

Healthcare payroll is the most layered payroll category in India. A single 200-bed hospital runs on at least five distinct workforce types - permanent staff doctors and nurses on monthly CTC under Section 192 TDS, visiting consultants and locum physicians on professional fees under Section 194J TDS, contract nursing and housekeeping agencies under CLRA Act 1970, ward boys and support staff almost entirely below the Rs 21,000 ESI wage ceiling, and apprentice or trainee paramedics with their own stipend rules. Each category has a separate pay structure, a separate statutory exposure, and a separate set of registers.

Patron Accounting LLP runs payroll for hospitals, multi-speciality chains, diagnostic networks, nursing homes, day-care centres, fertility clinics and pathology labs as a managed service. Scope covers shift differentials and night allowances mapped to attendance, Section 192 salary TDS for staff (Section 392 from FY 2026-27), Section 194J locum and consultant TDS processed in a separate batch (Section 393 from FY 2026-27), ESIC half-yearly returns with the December 2025 uniform wage definition applied, CLRA quarterly contractor reconciliation, Code on Wages 50 percent basic restructuring and NABH-ready credential expiry and POSH logs. Pricing starts at Rs 149 per employee per month.

Content is reviewed quarterly for accuracy.

Specialist healthcare payroll is required when one or more of the following apply:

• You operate a hospital, multi-speciality clinic, diagnostic chain, nursing home, fertility centre, IVF clinic or day-care under the Clinical Establishments Act 2010 (or state-equivalent).
• Your roster has three or more shifts with night, weekend and holiday differentials.
• More than 30 percent of your headcount earns gross wages below Rs 21,000 per month (ward boys, nursing assistants, housekeeping, dietary, security, lab support).
• You engage at least one contractor for nursing, housekeeping, security or dietary services under CLRA Act 1970.
• You pay visiting consultants, locum doctors or session-based specialists under Section 194J professional fees.
• You hold or are pursuing NABH or NABL accreditation requiring HR file readiness, credential expiry tracking and POSH case logs.
• You operate across multiple states (Delhi, Maharashtra, Tamil Nadu, Karnataka, Telangana) with different PT slabs and Labour Welfare Fund cycles.
• You are restructuring CTC under the Code on Wages 50 percent basic rule effective 21 November 2025.

Statutory Deadline Snapshot

• Monthly ESIC challan - 15th of following month
• ESIC Return of Contributions (half-yearly) - 12 November for April-September; 12 May for October-March
• Monthly EPF ECR - 15th of following month
• Monthly Section 192 / 392 salary TDS deposit - 7th of following month
• Monthly Section 194J / 393 locum and consultant TDS deposit - 7th of following month
• Quarterly Form 24Q / 138 (salary) - 31 July, 31 October, 31 January, 31 May
• Quarterly Form 26Q / 139 (locum and consultant) - same quarterly cycle
• Annual Form 16 / 130 (salary) by 15 June; Form 16A / 131 (194J) within 15 days of quarter-end
• Salary disbursement - within 7 days of period close (Section 17(1) Code on Wages)
• FnF settlement - 2 working days of last working day (Section 17(2))
• State Professional Tax - per state due date

Patron requires the following documents and registers from the hospital, clinic or diagnostic chain at onboarding:

• Hospital or clinic licence (Clinical Establishments Act registration / Shops and Establishment certificate)
• NABH or NABL accreditation certificate (if applicable) and last survey report
• CLRA Principal Employer Registration (Form II)
• Contractor licences (Form VI) and Form V issued by the hospital
• EPFO sub-code per facility and ESIC code per facility
• State Professional Tax certificate in each state of operation
• Labour Welfare Fund registration (state-specific - Maharashtra, Karnataka, Tamil Nadu, Gujarat etc.)
• Permanent staff master - PAN, Aadhaar, UAN, ESIC number, bank, designation, department, shift category, joining date, regime preference
• Locum and visiting consultant master - PAN, address, professional fee schedule, engagement letter, Section 194J consent
• Contractor master - agency name, MSA, scope of services, deployed-headcount monthly statement, last 12 months of wage register, PF and ESIC challans
• Department-wise shift roster templates with shift differential rates
• Last 12 months of ESIC challans, half-yearly Return of Contributions, EPF ECR, PT challans, TDS challans, Form 24Q and 26Q acknowledgements
• Credential expiry log - nursing licences, BLS / ACLS / NRP certifications, MCI registration of doctors, paramedic certifications
• POSH committee constitution and last 12 months of meeting minutes (NABH requirement)
• Creche compliance proof (if 50+ employees - Maternity Benefit Act)

If any of these are missing or expired, Patron handles renewal or fresh registration within the onboarding window. Share the inventory via WhatsApp at +91 945 945 6700 and we will revert with a missing-document checklist within 24 hours.

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 Healthcare Payroll consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

10,000+ Businesses Served  |  4.9 Google Rating  |  50,000+ Documents Filed  |  15+ Years Experience

Trusted by mid-sized multispeciality hospitals, diagnostic chains, fertility centres, day-care groups and NABH-accredited single-speciality units across Pune, Mumbai, Delhi NCR and Hyderabad. Sector coverage includes multi-speciality and single-speciality hospitals, fertility and IVF clinics, diagnostic and pathology networks, dental and dermatology chains, dialysis centres and standalone nursing homes.

Anonymised Outcome: A Pune-based 200-bed multispeciality hospital with three facilities, 480 permanent staff, 38 visiting consultants and four contract agencies (nursing, housekeeping, security, dietary) onboarded with Patron in Q4 2025. We separated the Section 194J locum batch from the salary batch, recovered Rs 6.2 lakh of cumulative PF short-remittance from the nursing agency via billing offset, restructured CTC under Code on Wages 50 percent rule for 80 percent of the permanent workforce in 5 weeks, and the NABH 5th Edition reaccreditation survey in Q1 2026 cleared with zero HR file observations.

4-Office Trust Signal: With offices in Pune, Mumbai, Delhi and Gurugram, Patron Accounting serves hospitals, clinics and diagnostic networks across India - both in-person and remotely.

Healthcare payroll links to several adjacent compliance workflows - all delivered by the same CA and CS team for a single point of accountability.

• Payroll Services (Parent Hub): Patron payroll hub across all industries - the umbrella under which healthcare payroll sits.
• Healthcare Sector Accounting Services: Bookkeeping, MIS, doctor settlement reconciliations and inventory accounting for hospitals and clinics.
• Statutory Audit: Companies Act audit covering employee benefit provisions, gratuity actuarial reconciliation, locum fee Section 40A(2) related-party disclosure and CLRA exposure.
• GST Refund: Export-of-services LUT and refund of unutilised ITC under Section 54 CGST Act for eligible categories (telemedicine to overseas patients, lab tests for foreign teleconsultations).
• PF Registration and Returns: EPFO sub-code activation for new facilities and monthly ECR filing.
• ESIC Registration, Calculation and Returns: ESIC code allocation, monthly contribution challan and half-yearly Return of Contributions.
• Professional Tax Returns: State PT returns across operating cities.
• ROC Notice Response: Annual ROC filings tying back to employee benefit disclosure and CLRA exposure.

ESI Act, 1948 (ESIC portal): Section 1 (extent), Section 2(9) (employee definition), Section 39 (contributions), Section 40 (employer recovery), Section 85 (prosecution for default). Wage ceiling Rs 21,000 under Rule 50, ESI (Central) Rules 1950 - last revised vide G.S.R. 1166(E) effective 1 January 2017.

Contribution Period: 1 April to 30 September and 1 October to 31 March under Regulation 4, ESI (General) Regulations 1950. Mid-period wage crossings continue contribution until end of half-period.

ESIC Contribution Rates: Employer 3.25 percent and employee 0.75 percent of wages (reduced from 4.75 percent and 1.75 percent effective 1 July 2019 per Gazette Notification No. 423(E)).

Contract Labour Act, 1970: Section 7 - principal employer registration. Section 12 - contractor licensing. Section 21 - principal employer liability for contractor wage default.

Code on Wages, 2019: Effective 21 November 2025 per Ministry of Labour and Employment notification. Section 6 - basic wages at least 50 percent of total remuneration. National floor wage applies.

Code on Social Security, 2020: Subsumes ESI Act 1948 and EPF Act 1952. Effective 21 November 2025; uniform wage definition for PF and ESI base from December 2025 - deems special allowance, CCA and medical allowance as wages if excluded components exceed 50 percent.

Section 192 IT Act 1961 (Section 392 IT Act 2025) (Income Tax Department TDS Compliance): Salary TDS at average slab rate; monthly deposit by 7th of following month.

Section 194J IT Act 1961 (Section 393 IT Act 2025): TDS at 10 percent on professional or technical fees; threshold Rs 30,000 per FY per payee. Applies to locum doctors, visiting consultants, radiologists and pathologists on session-based engagement.

EPF Act 1952 (EPFO): 12 percent each side on basic; EPF ECR by 15th of following month; Section 7A inspection for default; Section 14B damages up to 100 percent of arrears.

Factories Act, 1948: Applies to central kitchens, laundry units, sterilisation centres and other clinical-support "factories" of hospital groups. Section 51 (48-hour week), Section 59 (overtime at 2x), Section 79 (annual leave).

Maternity Benefit Act, 1961: 26 weeks paid leave for the first two children, 12 weeks thereafter; mandatory creche facility for establishments with 50+ employees.

Clinical Establishments Act, 2010: Central Act adopted state-by-state; registration mandatory for clinics, hospitals, diagnostic centres and day-care.

NABH 5th Edition Standards: HR documentation, credential expiry, mandatory training (CPR, BLS, infection control, fire safety), POSH committee and grievance log requirements.

Penalty Snapshot

• ESIC delayed-filing penalty - up to Rs 25,000 plus interest at 12 percent per annum on contribution dues
• ESI Act Section 85 - prosecution for default with imprisonment up to 2 years and fine
• CLRA Section 21 - principal-employer liability for contractor wage and PF / ESI default
• Section 201 IT Act - 1 percent per month non-deduction, 1.5 percent per month non-deposit
• Section 35(b) IT Act 2025 - 30 percent expense disallowance for TDS default
• EPF Section 14B - damages up to 100 percent of arrears
• Code on Wages Section 56 - up to Rs 1 lakh per violation

Three transitions hit healthcare payroll simultaneously. First, the December 2025 uniform-wage definition under the Code on Social Security 2020 has already expanded PF and ESI calculation base - hospitals not applying this are accruing under-contribution exposure each cycle. Second, the Income Tax Act 2025 takes over from 1 April 2026 - Form 16 becomes Form 130, Form 24Q becomes Form 138, Section 192 becomes Section 392, Form 16A becomes Form 131, Form 26Q becomes Form 139 and Section 194J becomes Section 393. Third, Code on Wages 2019 has been in force from 21 November 2025 - every CTC structure with basic below 50 percent of gross is accruing potential EPF and gratuity arrears.

Action now: book a payroll compliance review with Patron Accounting. We will run a free 30-minute audit covering Code on Social Security December 2025 wage definition impact, Section 192 / 194J to Section 392 / 393 transition readiness, and Code on Wages basic-pay restructure. Call +91 945 945 6700 or WhatsApp us.

Healthcare payroll in 2026 is the most layered payroll surface in India. Five workforce categories, three statutory codes simultaneously in transition (Income Tax Act 2025, Code on Wages 2019, Code on Social Security 2020), CLRA principal-employer liability for every nursing and housekeeping agency, locum doctor and visiting consultant fees taxed under a separate non-salary regime, an ESI ceiling that converts mid-period wage hikes into contribution-period puzzles, and an accreditation overlay (NABH or NABL) that turns HR documentation into a survey-grade audit trail - all on one monthly cycle.

Software-only platforms compute correctly when configured but the configuration burden, the locum batch separation, the contractor reconciliation and the NABH alignment stay with you. Patron Accounting LLP - a CA and CS practice with 15+ years of regulatory experience and offices in Pune, Mumbai, Delhi and Gurugram - delivers payroll for hospitals, clinics, diagnostic chains and nursing homes as a managed service starting at Rs 149 per employee per month.

The engagement includes salary plus locum batches, ESI half-yearly returns, CLRA quarterly reconciliation, Code on Wages restructure and NABH-aligned employee files. GST refund (for eligible service-export categories), statutory audit and accreditation overlay cross-sell deliver a single point of accountability across the full compliance perimeter.