The result, caused mainly by higher expenditure on joint Czech-EU projects and a capital injection for the state export insurer EGAP, compares to a 6.27 billion-crown surplus a year ago. At the end of March, the budget surplus had stood at 16.26 billion crowns.
Adjusted for funds from the European Union, the January-April budget would show a deficit of 21.9 billion crowns, compared to a deficit of 7.8 billion crowns at the same period last year.
Overal expenditure rose 8.6 percent while income was up 10.1 percent through the end of April.
Tax income rose 7.4 percent year-on-year to 376.98 billion crowns, including 89.28 billion in the value-added tax, up 4.5 percent year-on-year.
The 2018 central state deficit was approved by parliament with a 50 billion crown deficit.
The central government budget is the main part of the EU country's overall public sector finances, which also include local and regional administrations, the health insurance system and various off-budget funds.
The overall fiscal balance for last year has been estimated at 1.6 percent/GDP surplus and for this year the ministry expects it at +1.5 percent.