GST Compliance & Tax Invoicing

February 2026 · 6 min

Overview

Bio Ecko supports end-to-end GST compliance for Indian hospitals, including GSTIN configuration, HSN/SAC code mapping on services, automatic CGST/SGST computation on bills, and tax invoice generation in the prescribed format.

Most healthcare services are GST-exempt under SAC 9993, but certain services like cosmetic surgery, premium room rent, and cafeteria sales attract GST. Bio Ecko handles the mixed-tax scenario seamlessly.

Setting Up GST

Step 1 -- Organization GSTIN: Go to Settings > Organization Profile and enter your hospital's 15-digit GSTIN. This is printed on all tax invoices.

Step 2 -- State Code: The first two digits of GSTIN determine the state code. This is used to decide intra-state (CGST + SGST) vs. inter-state (IGST) taxation.

Step 3 -- HSN/SAC Codes on Services: Go to Billing > Fee Schedule. For each service item, set:

• HSN/SAC Code (e.g., SAC 999311 for medical consultation, SAC 999312 for surgical services)
• GST Percentage (0% for exempt, 5%, 12%, or 18% for taxable items)

The system pre-fills common codes, but you should verify against the latest GST council notifications.

Step 4 -- Medicine HSN Codes: Medicines in the pharmacy already have an HSN Code field. Common codes:

• 3004 -- Medicaments (dosage form)
• 3006 -- Pharmaceutical preparations
• 9018 -- Medical instruments and appliances

CGST and SGST Calculation

For intra-state supplies (patient and hospital in the same state):

• CGST = GST Rate / 2
• SGST = GST Rate / 2

Example: Service at 18% GST on INR 10,000 taxable value:

• CGST @ 9% = INR 900
• SGST @ 9% = INR 900
• Total Tax = INR 1,800
• Invoice Total = INR 11,800

For inter-state supplies (rare in hospitals, typically for corporate billing to out-of-state entities):

• IGST = Full GST Rate

The system determines intra vs. inter-state automatically based on the hospital's state code and the billing address.

Tax Invoice Format

Every bill with taxable items generates a GST-compliant tax invoice containing:

1. Supplier Details -- Hospital name, address, GSTIN, state code
2. Recipient Details -- Patient name, address (and GSTIN if applicable, e.g., corporate billing)
3. Invoice Number -- Sequentially numbered (same as bill number)
4. Invoice Date
5. Item-wise Breakdown:
   • Description of service/goods
   • HSN/SAC code
   • Quantity and unit
   • Rate per unit
   • Taxable value
   • CGST rate and amount
   • SGST rate and amount
6. Summary:
   • Subtotal (taxable value)
   • Total CGST
   • Total SGST
   • Total tax
   • Grand total
   • Amount in words

The tax invoice can be printed or downloaded as PDF from the bill detail screen.

Exempt vs. Taxable Services

GST-Exempt Healthcare Services (0% GST):

• Doctor consultation fees
• Diagnostic tests (blood tests, X-ray, MRI, CT, ECG, etc.)
• Surgical procedures (non-cosmetic)
• Room rent below INR 5,000 per day
• ICU/NICU/CCU charges
• Nursing charges
• Ambulance services
• Blood bank services

Taxable Services:

• Room rent at or above INR 5,000 per day -- 5% GST (without ITC)
• Cosmetic surgery and hair transplant -- 18% GST
• Cafeteria / canteen services -- 5% GST
• Pharmacy sales (retail, not part of treatment) -- 5% / 12% / 18% based on HSN
• Medical equipment rental -- 18% GST

Important: When room rent crosses INR 5,000/day, GST applies only to the room rent, not to all services during the stay. Bio Ecko handles this automatically.

GST Reports

Bio Ecko generates the data needed for GST returns:

• GSTR-1 Data -- Outward supplies with invoice-wise details, HSN summary, and state-wise summary
• GSTR-3B Data -- Summary of outward/inward supplies, ITC claimed, and tax liability
• HSN-wise Summary -- Aggregate taxable value and tax collected by HSN/SAC code
• Monthly Tax Liability -- CGST, SGST, and IGST collected per month

Export these reports in Excel format for upload to the GST portal or for your CA to file returns.

Notes

Related topics