The amendment to the Tax Code effective from 1 July 2025 has extended the possibilities of waiving penalties that arise, when an additional tax is assessed ex officio. Before the amendment, the tax administrator could waive penalties up to a maximum of 75%. The tax administrator may now waive 100% of the penalty incurred from 1 July 2025 on a taxpayer for a justifiable reason. At the same time, however, the Tax Code has retained the possibility of waiving penalties of up to 75% in cases where there is no justifiable reason, but the taxpayer has duly cooperated with the tax administrator as part of the control procedure leading to the additional assessment.
Following the amendment to the Tax Code, the General Financial Directorate issued a new instruction GFR-D-72 on the waiver of tax accessories, which came into force on 15 September 2025. The Instruction sets out the procedure of the tax administrator in the waiver and unifies administrative practice in assessing justifiable reasons on the basis of which tax accessories can be waived.
According to the Instruction, a justifiable reason for waiving the 100% penalty is a situation where the taxpayer filed an inadmissible additional tax statement before the commencement of the audit procedure and used the data claimed by the tax administrator therein to determine the resulting tax, while the additional tax assessed does not exceed twice the tax claimed by the taxpayer. The condition for maximum waiver is the fulfilment of other formal and substantive conditions for waiver, as in the case of waiver only up to 75% of the penalty.
An inadmissible tax return may be filed if the taxpayer files an additional tax return at a time when the tax administrator has not yet managed to determine the tax on the basis of a previously filed tax return. In such a situation, the Tax Code stipulates that the tax administrator will use the data from the ineffective tax return as if it were its own findings, which results in a penalty in the event of a higher tax liability. This negative consequence is to be eliminated through the institute of waiver of penalties.
The instruction itself then allows the tax administrator to waive penalties for a justifiable reason other than the one specified in the instruction. However, in such a case, it will be a waiver beyond the scope of the Guideline, which is subject to de minimis rules regulated by EU law, e.g. the maximum amount of aid in different fields of activity, which applies to the entire affiliated group of companies.
Instruction GFR-D-29 on the waiver of fines for failure to submit a control statement has also been updated, to which a new justifiable reason for waiver has been added. According to it, the taxpayer has the possibility of a general waiver of one error related to the fulfilment of obligations in the control statement and constituting the occurrence of a fine. This justifiable reason applies to an error occurring from 1 January 2025 in the case of a fine determined pursuant to Section 101h (1) c) and d) of the Value Added Tax Act.
Once per calendar year, the tax administrator may, at the request of the taxpayer, waive one fine for failure to file a subsequent control statement based on a request from the tax administrator to change, supplement or confirm the data stated in the submitted control statement (CZK 30,000) or a fine for failure to file a control statement within the specified deadline based on a request from the tax administrator (CZK 50,000). The condition for a general waiver is the fulfilment of other formal and substantive conditions.
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