Running a healthcare business is demanding. Whether you manage a private clinic, dental practice, pharmacy, or wellness centre, your focus is on patients, not paperwork. But with the Inland Revenue Board of Malaysia (IRBM) rolling out mandatory e-invoicing, compliance is now a priority that can’t be ignored.

Starting in 2024, healthcare businesses will be required to issue e-invoices for income and expenditure, as part of the national push toward digital tax reporting. While this aims to reduce fraud and improve transparency, it also adds new layers of cost, system changes, and cash flow challenges, especially for smaller operators.

In this guide, we break down how e-invoicing applies to the healthcare sector, what types of transactions are affected, and how to stay compliant without disrupting your day-to-day operations. We also share how Funding Societies can help with financing options designed for SMEs in healthcare.

To learn more about the e-invoicing initiative or compare how the guidelines differ by industry, read our e-invoicing Malaysia guide here

What E-Invoicing Means for the Healthcare Sector

From 1 August 2024, companies with over RM100 million in annual revenue must begin issuing e-invoices. Other businesses, including healthcare providers, will follow in stages based on revenue thresholds. Check your business’s mandatory e-invoicing start date here.

For healthcare SMEs, e-invoicing means:

  • Every consultation, treatment, or sale of medication must be recorded with an official e-invoice
  • Payments from insurance panels, government programmes, and patients need proper tracking
  • Expenses like equipment rental, medical supplies, or outsourced services must be supported with digital invoices

Whether you run a dental clinic, TCM centre, or chain of optical stores, your financial records must now be cleaner, more transparent, and ready for IRBM audit.

Healthcare Transactions That Require E-Invoices

Based on IRBM’s healthcare-specific guidelines, here are the transaction types that require e-invoices:

Income-Generating Transactions:

  • Patient consultation fees (in-person or virtual)
  • Sale of medicine, health supplements, and medical equipment
  • Laboratory tests and diagnostics
  • Medical procedures and treatment packages
  • Services provided to panel insurers or corporate clients
  • Traditional and complementary medicine (TCM) services

Expenses That Require E-Invoices:

  • Purchase of pharmaceuticals and medical consumables
  • Salaries or contract fees for locum doctors and specialists
  • Equipment maintenance and lease costs
  • Third-party laboratory services
  • Clinic management software or telehealth platforms
  • Marketing, utilities, and insurance expenses

Properly issued and stored e-invoices help reduce tax errors, rejected claims, and manual admin.

For the most up-to-date and detailed e-invoicing for healthcare information, refer to the official guideline.

Special Scenarios in Healthcare E-Invoicing

Healthcare operations often involve mixed payment models, packages, and refunds. Here’s how some of those scenarios are handled under IRBM’s e-invoicing rules:

Panel Patients (Insurance/Corporate):
Issue the e-invoice to the insurer or corporate client, not the patient. The invoice should reflect services rendered and payment terms agreed.

Medical Packages (e.g. screening, prenatal care):
E-invoice can be issued as a lump sum or itemised, but must be aligned with actual services delivered.

Deposits and Prepaid Treatment:
Issue an e-invoice for the deposit when received. Once the treatment is provided, issue a final e-invoice for the completed service.

Refunds and Cancellations:
A credit note must be issued via e-invoice to reflect any refund or cancelled appointment. Learn how credit notes and validation work in the e-invoicing process.

How to Implement E-Invoicing: Steps for Healthcare Providers

You don’t need to overhaul your clinic overnight. Here’s how to phase in the changes:

Step 1: Assess Your Current System

Check if your clinic management software or POS supports e-invoicing or IRBM integration. You may need an upgrade or API connector. Make sure your e-invoice format meets IRBM’s e-invoicing compliance requirements.

Step 2: Choose a Compliant Provider

Use a provider listed under IRBM’s MyInvois system that supports invoice validation, corrections, and secure storage.

Step 3: Set Internal Billing Procedures

Map out how your team handles deposits, walk-ins, panel claims, and refunds. Standardise when and how e-invoices are issued.

Step 4: Train Your Team

Ensure front-desk staff, finance, and operations understand e-invoicing steps and documentation requirements.

Step 5: Start Small and Scale

Pilot the process with one service category (e.g. outpatient services) before rolling it out across the business.

Funding Societies: Helping Healthcare SMEs Stay Liquid During the E-Invoicing Transition

While e-invoicing will lead to cleaner financials and better compliance, the shift brings added costs — and for many healthcare SMEs, those costs hit hard.

You may face:

  • Software upgrade costs for clinic systems or e-invoicing platforms
  • Training expenses for front-line and back-office staff
  • Delayed payments from insurers or corporate clients, even after e-invoicing is implemented
  • Cash flow pressure from having to pay salaries, suppliers, and lab partners upfront
  • Limited working capital during a time when you’re also investing in digitalisation

This financial strain can lead to deferred expansion, staff burnout, or slower turnaround times — especially if your working capital is tight.

Funding Societies offers tailored financing solutions to help:

Invoice Financing 

Convert your issued e-invoices into upfront working capital of up to RM1 million. With financing of up to RM1 million and flexible tenures, use it to cover salaries, medicine restocks, or rent while waiting on payments from insurers or corporate clients.

Micro Financing

Quick, collateral-free financing of up to RM200,000 for healthcare operators. Ideal for covering software upgrades, onboarding costs, or cash flow gaps during quieter months.

Islamic Financing Options

Shariah-compliant options are available for businesses seeking ethical financing solutions. Suitable for clinic operators and health brands looking to expand or stay operational without riba.

Don’t let invoicing delays or system costs disrupt patient care. Plan ahead and use flexible financing to stay competitive and compliant.

Final Thoughts: E-Invoicing Can Simplify, Not Slow You Down

With the right setup, e-invoicing can help your healthcare business save time, reduce errors, and stay compliant. However, like any system change, it requires planning, training, and a steady cash flow to implement smoothly.

Funding Societies is here to help your clinic or healthcare brand stay financially strong while adapting to these new rules.