The penalty for a late VAT return filing is 0,05% of the payable amount per day. However, the Tax Authorities impose those penalties, only if the penalty would be 1000 CZK or higher. If the amount is less, no penalty will be imposed.
Moreover, for a late payment interest costs are calculated. The interest rate now is 11,75%, but it might differ depending on the current rates set by the Czech National bank.