A VAT tax audit is the procedure by which the tax authority verifies that declared VAT is correct, focusing above all on the right to deduct input VAT. In both Slovakia (Tax Code, Act No. 563/2009 Coll.) and the Czech Republic (Tax Code, Act No. 280/2009 Coll.) inspectors cross-check your VAT return against a control statement and your partners’ data, ask for invoices and evidence that the supply actually took place, and put the burden of proof largely on you. The procedural details differ: Slovakia caps an audit at one year and adds interest of at least 15% on assessed tax, while the Czech Republic imposes a 20% penalty and interest of 11.75% a year in the second half of 2026.
What do the two tax authorities check in a VAT audit?
In both countries the audit is less about arithmetic and more about substance: the inspector wants proof that a real transaction sits behind each figure. The core issue is the right to deduct input VAT — whether the supplier genuinely provided the supply, whether you used it for your taxable activity, and whether the deduction was therefore legitimate. This is where most disputes arise.
The main matching tool has different names but the same purpose. Slovakia uses the VAT control statement (kontrolný výkaz) and the Czech Republic the control statement (kontrolní hlášení); both let the authority pair each transaction between supplier and customer, so a mismatch or an unreported supply on the other side flags your deduction. For cross-border trade, both administrations also check the recapitulative statement and the partner’s VAT number in the VIES system.
How does the audit procedure work?
In Slovakia an audit usually starts with a formal notice stating the start date and the periods and tax concerned; if you cannot attend on the day, you have 8 days from delivery to notify an obstacle and agree a new date. The audit is capped at one year from its start under Section 46(10) of the Tax Code and ends with a protocol (Section 47), to which you may respond in writing within a period of at least 30 working days.
In the Czech Republic the audit is governed by Sections 85 and following of the Tax Code and runs as an evidentiary process within the three-year assessment period. It ends not with a protocol but with a tax audit report (zpráva o daňové kontrole) under Section 88, which the tax authority discusses with you before it becomes final.
Which documents should you prepare?
The practical advice is identical in both jurisdictions: assemble a paper trail from which the whole transaction can be reconstructed, not just the invoice. Because the burden of proof lies mainly with the taxpayer, a single missing document usually turns into a dispute over the deduction. For each period under review you should have ready:
- received and issued invoices with all mandatory tax-document details;
- the control statement and recapitulative statement for the audited periods, plus the filed VAT returns;
- contracts, orders, delivery notes and handover protocols;
- bank statements and proof of payment;
- VAT records and the accounting entries for each supply.
Slovak invoice requirements are set out in Section 74 of the Slovak VAT Act (Act No. 222/2004 Coll.) and the Czech ones in the Czech VAT Act (Act No. 235/2004 Coll.); both require the parties’ details and VAT numbers, the tax base, the rate and the amount of tax. Reviewing invoices continuously, rather than only when a notice arrives, is the cheapest form of audit insurance.
What happens after the audit and what does it cost?
The biggest difference shows up in the sanctions once tax is assessed. In Slovakia, an assessed difference triggers interest on arrears under Section 156 (at least 15% a year) and a penalty tied to the amount of additional tax, which can never exceed that tax itself. In the Czech Republic, a separate penalty of 20% of the additionally assessed tax applies under Section 251 — but only when the authority assesses the tax of its own motion, typically after an audit — alongside interest under Section 252 of the ČNB repo rate plus 8 points, i.e. 11.75% a year in the second half of 2026.
In both countries the lesson is the same: a voluntary correction filed before the inspector finds the error is dramatically cheaper. In the Czech case a supplementary return avoids the 20% penalty entirely, and in Slovakia it sharply reduces the penalty rate on the difference.
Have you received notice of a VAT tax audit in Slovakia or the Czech Republic, or do you want to check in advance whether your documents will hold up? We will review your invoices, control statements and input-VAT deductions, prepare the file and represent you before the tax authority.
FAQ
What do inspectors check most in a VAT audit?
The focus in both Slovakia and the Czech Republic is the right to deduct input VAT — whether the supplier really provided the supply and whether you used it for your taxable activity. The authority cross-checks your control statement against your partners’ data, verifies VAT numbers in VIES and asks for invoices and evidence of the supply. The burden of proving that the transaction actually happened lies mainly with the taxpayer.
How long can a VAT audit last?
In Slovakia the audit is capped at one year from its start under Section 46(10) of the Tax Code and ends with a protocol you may comment on within at least 30 working days. In the Czech Republic there is no one-year cap, but the tax can generally be assessed only within a three-year period, and the audit ends with a tax audit report under Section 88 rather than a protocol.
What penalties apply if the audit finds under-declared VAT?
In Slovakia an assessed difference carries interest of at least 15% a year under Section 156 plus a penalty linked to the additional tax, capped at that tax. In the Czech Republic a 20% penalty under Section 251 applies when the authority assesses the tax of its own motion, along with interest of 11.75% a year in the second half of 2026. In both countries a voluntary supplementary return filed first is far cheaper.