How Medical Organizations Should Account for VAT and CIT in 2026 - FCHAIN

How Medical Organizations Should Account for VAT and CIT in 2026

 Starting January 1, 2026, new taxation rules for medical organizations regarding VAT and Corporate Income Tax (CIT) came into force in Kazakhstan. The changes affect medical services, the sale of medicines and medical devices, as well as the application of tax exemptions and rates.

 

VAT on Medical Services in 2026

VAT Exemption

According to Article 474 of the Tax Code of the Republic of Kazakhstan, the following transactions are exempt from VAT:

1. medical services;
2. pharmaceutical products,

if they are provided within: the Guaranteed Volume of Free Medical Care (GVFMC), Mandatory Social Health Insurance (MSHI) and treatment of orphan and socially significant diseases.

The exemption applies only:

1. to healthcare entities;
2. with a valid medical license;
3. for services and goods included in the lists approved by Resolution No.1203 dated December 31, 2025.

 

VAT Exemption on Import

According to Article 479 of the Tax Code, imports of pharmaceutical products are exempt from VAT if imported for:

1. GVFMC;
2. MSHI;
3. treatment of orphan and socially significant diseases.

The list and exemption procedures are also approved by Resolution No.1203.

 

VAT Rates in 2026

16% VAT Rate

The standard VAT rate in Kazakhstan in 2026 is 16%, unless otherwise provided by the Tax Code.

5% VAT Rate

According to Article 503 of the Tax Code, the 5% VAT rate applies to:

1. 1. Sale and import of:

• ~ medicines (except exempt ones);
• ~ medical devices;
• ~ medical device components;
• ~ technical assistive devices.

The list is approved by Resolution No.1204 dated December 31, 2025.

1. Medical services

The 5% VAT rate applies to medical services provided:

• ~ by healthcare entities;
• ~ with a valid medical license.

At the same time, the 5% rate does not apply to services exempt under Article 474 of the Tax Code.

 

How to Reflect VAT in Form 300.00

In the VAT declaration (Form 300.00), line 300.00.001 reflects:

• ~ turnover taxed at 16%;
• ~ turnover taxed at 5%.

Input VAT Credit

According to Article 480 of the Tax Code, medical organizations may claim VAT credits:

• ~ based on electronic invoices from suppliers;
• ~ based on import VAT.

The main condition is that goods, works, and services must be used for taxable turnover.

 

Corporate Income Tax for Medical Organizations in 2026

5% CIT Rate

According to Article 357 of the Tax Code, a 5% CIT rate applies to organizations operating in the social sector in 2026.

Organizations Classified as Social Sector Entities

According to Article 15 of the Tax Code, a legal entity is considered a social sector organization if:

• ~ at least 90% of annual gross income is derived from social sector activities;
• ~ it has a medical activity license.

Medical services are classified as social sector activities.

Income Included in the 90% Calculation

The following income is also included: charitable assistance, sponsorship assistance, gratuitous receipts, membership fees, bank deposit interest, positive foreign exchange differences.

 

When the 20% CIT Rate Applies

The 20% CIT rate applies:

• ~ if Article 15 conditions are not met;
• ~ to activities unrelated to the social sector;
• ~ to the sale of medicines and medical devices.

 

Conclusion

In 2026, medical organizations must carefully approach VAT and tax accounting issues. It is important to properly distinguish exempt turnover, turnover taxed at 5%, and transactions subject to the standard 16% VAT rate.

Organizations must also: properly account for input VAT, choose the appropriate VAT credit allocation method and analyze income structure to apply the preferential 5% CIT rate.

Errors in applying tax rates, exemptions, and accounting procedures may lead to additional tax assessments, penalties, and tax risks during audits.

 

Accounting and Tax Services from FChain

FChain provides professional accounting and tax services for medical organizations in Kazakhstan. We support clinics, medical centers, and other healthcare entities in accounting and tax matters considering all legislative changes in Kazakhstan.

We offer:

• – correct determination and application of VAT rates;
• – accounting support for clinics and medical centers;
• – preparation and review of VAT declarations (Form 300.00);
• – accounting outsourcing;
• – tax reporting preparation and tax risk reduction.

FChain is a reliable partner for the medical business in Kazakhstan.

Property Tax: What Has Changed for Legal Entities and Individual Entrepreneurs

Prepared by: Moldir Mukhtar

Business Development Specialist

FChain Kazakhstan

 

📩 almaty@f-chain.com
📱 WhatsApp: +7 771 214 1820