Last year, the budget ended June with a 5.9 billion crown deficit.
The year-on-year drop is caused mainly by higher income of European Union funds last year when the last EU budget period financing was being completed, the Finance Ministry said.
Also this year, more than half of some payments were already made by June, including contributions to the EU budget or payments to regional budgets, the ministry said.
Adjusted for funds from the EU, the end-June budget would show a deficit of 22.8 billion crowns, versus 28.4 billion crowns deficit at the same period last year.
Overal expenditure rose 10.2pc while income was up 8.1pc. Tax revenue rose 6.8pc year-on-year.
Value-added tax collection rose 3.0pc year-on-year to 135.5 billion crown.
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.