Nine other people who had also been arrested have been released by the investigating judge, the federal prosecutor’s office said.
Searches were conducted overnight in 16 municipalities, mainly around Brussels, with checks on 152 lock-up garages.
PM Charles Michel said security would be stepped up at public events.
He tweeted (in French) after a meeting of the Belgian security council to say events would go ahead as planned, urging the public to remain calm.
Belgian media had earlier reported that militant Islamists may have been planning to attack the football fan zone in Brussels, where Belgium’s games in the Euro 2016 tournament in France are screened.
On 22 March, bombs killed 32 people at a Brussels airport and a metro station.
The three men charged on Saturday were named as Samir C, aged 27; Moustapha B, 40; and Jawad B, 29.
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Image courtesy of AP