What is a VAT control report: who submits, deadlines and frequency

Thanks to our article, you will get an answer to what a VAT control report is and what it is used for. You will find out who files it and who doesn’t, as well as its frequency. You will learn the exact deadlines for filing, the rules for subsequent control statements and the deadlines for responding to a call. You will get practical guidance on how to file technically in EPO/My Taxes and why it is crucial to follow the prescribed XML format. Finally, you’ll learn what penalties there are in 2025 and how the control return differs from the VAT return and the summary return.

What is a VAT control report

A control report (CR) is a separate electronic VAT return. It is not a substitute for a VAT return or a summary report, but is a special summary of data from your tax documents (issued and received) that helps the tax authorities to match transactions between taxpayers and to target possible fraud. It is a special tax statement within the meaning of the Tax Code, but it does not determine the amount of tax itself – it serves as a control against your VAT return. It is submitted exclusively electronically and in the prescribed structure.

In other words, the VAT control statement is a “data fingerprint” of selected data from your VAT records. This allows the tax authorities to compare whether the supplier and the customer have reported the same transaction and, if they find a discrepancy, ask you to explain or correct it.

Who submits control reports

The basic rule is straightforward: the control report is submitted by VAT payers registered in the country, regardless of whether they are domestic or foreign. The control report is submitted by the representative member of the group on behalf of a group of connected persons. On the other hand, it is not filed by an identified person, a person who is not a VAT payer, a payer with no supplies in the period concerned (typically when he reports neither supplies received nor supplies made) and a payer who only makes exempt supplies without entitlement to deduction.

In practice, this means that you file a control report for each period in which:

• you declare output tax (typically on domestic taxable supplies),
• you claim a deduction on taxable supplies received,
• you report transactions under the reverse charge regime,
• where applicable, reporting selected transactions related to investment gold.

Example: a Czech Ltd. issues three domestic invoices with tax in January and receives two invoices with a claim for deduction. It must file an audit return for January, even if the resulting tax return comes out to zero (typically when the outputs and deductions match). The obligation to file a control report is linked to the existence of reportable transactions, not to the amount of tax.

Control statements and frequency

Here we must distinguish between legal persons and natural persons (self-employed persons):

1. Legal persons submit a control report every calendar month, regardless of whether they are monthly or quarterly VAT payers. Practical consequence: even a “quarterly” limited company sends a control report every month.
2. Individuals (self-employed persons) submit control statements at the same frequency as VAT returns – i.e. monthly or quarterly depending on their tax period. Therefore, a self-employed person with a monthly period sends the control report every month, a quarterly taxpayer once a quarter.

This distinction can be tricky and leads to errors for companies that switch to a quarterly tax period and mistakenly believe that the control report will also be submitted quarterly. It will not – for legal entities the control report always remains monthly.

Deadline for filing the control report

The deadline for filing the control report depends on the type of entity and the frequency:

• Legal entities: by the 25th day after the end of the calendar month for which the QR is submitted (i.e. QR for January by 25 February). Still monthly.
• Natural persons: within the deadline for filing VAT returns, i.e. monthly or quarterly, always by the 25th day after the end of the tax year (e.g. for the first quarter by 25 April).

If you find an error after filing, a ‘ follow-up’ report is due. You must submit it within 5 working days of discovering the incorrect or incomplete information. This fulfils your legal obligation to correct the data after the deadline for a proper QR.

How to submit a control report

The VAT control report must be submitted exclusively electronically in the prescribed format and structure. In practice, you will either use the electronic form in the EPO application on the My Taxes portal or export from the accounting system to XML. If you send by data mail, you must supply the XML in the prescribed structure.

In the past, there has been a discussion about the constitutionality of fines related purely to non-compliance with the electronic format according to the internal instruction of the GFD. However, for the practice in 2025, always send the control reports in the currently required XML – you will avoid unnecessary disputes and calls for correction.

What is reported in the control report

The control report is divided into parts (A/B) and sections according to the type of transactions and values.

Typical example: you are a monthly taxpayer – self-employed and in January you issued three invoices to domestic VAT payers and received two invoices from your taxpayer suppliers. In addition, you have one invoice in reverse charge (e.g. construction work) – you show this in the relevant section of the reverse charge. You will submit your control report for January by 25 February (as a monthly payer). You will submit your VAT return by the same deadline. The order of submission is irrelevant.

Corrections, challenges and subsequent control statements

If the tax authorities become aware of an irregularity (for example, the counterparty has declared a different amount), they will invite you to submit a subsequent control report. In it , you confirm the accuracy of the original data or correct it. You must respond to such a notice: within 17 days of the date of delivery to your mailbox or within 5 working days of notification of the notice (if it is not delivered by mailbox).

Irrespective of the notice, if you yourself discover incorrect or incomplete data after the deadline for proper control reporting has passed, you are obliged to submit a subsequent control report within 5 working days from the date on which you discovered the error. The subsequent control report shall be submitted for the entire period concerned and shall replace the original data.

Penalties and waivers: what penalties are available and when to apply for relief

The penalty system for the VAT control declaration is set out quite strictly in the VAT Act, with the basicpenalties arising directly from the law once a given event (e.g. missing a deadline) has occurred. In 2025, you may receive the following penalties:

• cZK 1,000 if you file a control report after the deadline without a request from the tax authority.
• cZK 10,000 if you file the control report within the deadline after the tax authority’s invitation.
• cZK 30,000 if you fail to submit a subsequent control report following a request to complete/correct or confirm the data.
• 50 000 CZK if you do not submit the control report even within the alternative period after the invitation.

Half the amount of fines can fall on individuals, legal entities with a quarterly tax period and one-member LLCs with a natural person partner (if they meet the statutory conditions). In addition, the tax administrator may impose up to CZK 50,000 in the event of non-compliance with a notice to remove doubts and up to CZK 500,000 in the event of serious obstruction of tax administration.

Audit report vs. return vs. summary report

• Control report: control tool – data from documents, matching between taxpayers; submitted electronically in XML; does not calculate tax.
• VAT return: tax statement where you calculate output tax and input tax deductions; frequency by tax period.
• Summary statement: mainly related to cross-border transactions in the EU; submitted monthly by the identified person if obliged to do so.

Summary

The control report is a separate electronic VAT submission which matches data from issued and received documents and serves as a check against the VAT return. It is submitted only by VAT payers registered in the Czech Republic for the period in which they have reportable supplies. Legal entities always send the KH monthly, self-employed persons send it according to their tax period (monthly or quarterly). The deadline is by the 25th day after the end of the period; it is submitted only electronically in the prescribed XML. If you discover an error after the deadline, you must submit a follow-up KH within 5 working days of discovery; you must respond to the tax administrator’s request within the statutory deadlines.

The KH reports selected data from the documents (Part A – outputs, Part B – deductions, including the reverse charge scheme). Basic penalties in 2025: CZK 1,000 for late filing without a notice, CZK 10,000 after a notice within the alternative deadline, CZK 30,000 for failure to file a subsequent KH as requested and CZK 50,000 for failure to file even within the alternative deadline; furthermore, up to CZK 50,000 for failure to remove doubts and up to CZK 500,000 for serious obstruction of tax administration.