In the context of the measures taken by the government in response to the spread of the coronavirus epidemic, the government has also taken measures concerning payers of value added tax. The government’s decision also “freed up obligations” in the area of filing control statements and VAT returns.
Taxpayers are obliged to submit a control statement for the relevant calendar month within 25 days after the end of that month if they are legal entities or within the deadline for filing a tax return if they are private individuals. In the case of late submission of the control statement, the payer is subject to a penalty. In view of the current situation, the Ministry of Finance has issued a decision whereby, in the event of late submission of the control statement, the taxpayers will be exempted from the penalty. It is therefore only a waiver of the penalty for late submission of the control statement, not a postponement of the deadline for submission. However, this pardon from the Ministry of Finance applies only to penalties where the obligation to pay them arose in the period from 1 March 3. 2020 to 31 July 7. 2020.  If the application for the remission of a penalty for failure to submit the control statement is filed by 31 July 7. 2020, the filing of the application will be exempt from the administrative fee.
It should be noted that this is a waiver of the penalty for failure to file a control statement, where the taxpayer subsequently files the control statement without being invited to do so by the relevant tax office, i.e. the first penalty of CZK 1,000. This penalty will be waived automatically. If, however, the penalty is incurred on the basis of other facts, such as the submission of the control statement only within the additional time limit set by the tax office, an individual application for remission will have to be submitted, specifying the reasons for not submitting the control statement and, in particular, justifying how these reasons are related to the current situation regarding the spread of the coronavirus (i.e. the following penalties of CZK 10,000, CZK 30,000 or CZK 50,000, which will be determined by a payment assessment).
In the case that the taxpayer, on the basis of an individual application, has asked for a waiver of the penalty for failure to submit the control statement (i.e. a penalty of CZK 10,000, CZK 30,000 or CZK 50,000) and the application was at least partially granted and the taxpayer files the tax return, even though late, the penalty for the failure to file the value added tax return will be automatically waived for the tax period which is at least partially identical to the period for which the control statement (for which the penalty was waived) was filed. However, the filing of the tax return must take place no later than the day on which the late filing of the related control statement occurs. 
In the case of a decision on the remission of a penalty on the basis of an individual application in relation to the spread of the coronavirus, a special guideline has been issued by the General Financial Directorate, which the tax authorities must follow.  It is important to note that the tax authority also examines in this case whether the applicant has not seriously violated tax or accounting regulations, and the applicant must credibly prove that the obligation to pay the penalty arose as a result of extraordinary measures related to the spread of the coronavirus. The decision does not therefore automatically entitle a person to the remission of the penalty, but rather extends the list of justifiable reasons that may lead to its remission or reduction. Thus, even though there was a nationwide quarantine measure, but it did not significantly affect the business, this fact will have no effect in this case and the penalty will not be reduced or waived. On the other hand, if as a result of the measure the entrepreneur had to care for a member of his or her household or was ill himself or herself, for example, the penalty will be partially or completely waived. Anything that will be of testimonial value as to the facts in question may then be used to prove those facts.
The application for remission of the penalty is not submitted on any special form and thus there is no prescribed form. However, it is important to make sure that the submission makes it clear who is making the submission (identification of the taxable entity), what it concerns (penalty for failure to submit a control statement according to a payment assessment) and what it proposes (remission of the penalty). The application must be submitted within three months of the date of the legal force of the payment assessment deciding on the obligation to pay the relevant penalty. The application can be submitted at any branch of the tax office according to the place of residence of a natural person or the registered office in the case of legal entities. Ideally, however, you should apply directly to the local authority that will deal with the application.
 Decision on the remission of interest, fees and other charges related to tax and administrative fees due to an extraordinary event of 16 March 3. 2020, Ref. No. MF-7108/2020/3901-2.
 Decision on remission of interest, fees and other charges related to tax, tax prepayments and administrative fees due to an extraordinary event of 24 March 2020, Ref. No. MF-7633/2020/3901-2. 3. 2020, Ref. No. MF-7633/2020/3901-2.
 GUIDELINE No. GFŘ–D–44 on remission of default interest, interest on overdue amounts and penalty for failure to file control statements, Ref. No. 18787/20/7700-10123.