The result compares to a 0.8 billion crown surplus recorded a year ago when the budget was helped by European Union fund payments.
Adjusted for EU funds, the end-April budget would show a deficit of 27.2 billion crowns, versus 21.7 billion crowns deficit in the same period last year, the data showed.
Overall expenditure rose 13.4 percent while income was up only 6.5 percent.
The 2019, central state deficit was approved by parliament with a 40 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 ministry forecasts the overall fiscal balance to show a 0.3 percent/GDP surplus this year before falling to its first deficit since 2015, next year, to a 0.2 percent of GDP gap.