The ministry said in a statement that the deficit for the first four months of the year represented 29.7 percent of the targeted deficit for the full year compared with 31 percent in the same period of 2015.
The primary surplus, which excludes debt servicing costs, reached 1.118 billion euros, an improvement of 261 million euros compared with the same period last year.
Expenditure rose 0.7 percent between January and April, below a rise of 5.7 percent foreseen in the government's budget for 2016. Revenues rose 0.5 percent.
Last year, Portugal cut the budget deficit to 4.4 percent of GDP from 7.2 percent in 2014, but overshot its target of around 3 percent of GDP due to Lisbon's second bank rescue in as many years.
The European Commission has warned that it may penalise Portugal for last year's overshoot.
The left-leaning government, which took power in late 2015 and started reversing austerity policies of the previous administration, says it will meet this year's budget deficit goal of 2.2 percent of gross domestic product.