The arrests come after six raids in the towns of Vilvoorde and Machelen, near Brussels, as part of a probe launched in 2013, the Brussels federal prosecutor's office said.
Police also seized suspicious materials, it said in a statement. All of the suspects, who are in their twenties, were remanded in custody.
Belgian authorities issued an arrest warrant for a fourth suspect believed to be in Syria.
Belgium has produced the highest number of so-called foreign fighters per capita of any EU member state, an estimated 325, according to officials.