The raids occurred as Belgium remained on high alert following deadly jihadist bombings in March and a machete attack against police officers a week ago.
"All three were released," Eric Van Der Sypt, a spokesman for the federal prosecutor's office, told AFP.
A judge decided there was not enough evidence to keep them in custody.
The three, identified as Wassime A., Asma A. And Malika B., were detained following eight raids Wednesday night that were ordered by a judge investigating terrorism cases.
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Van Der Sypt also said the raids were not linked to an investigation into another "possible threat" the prosecutor's office mentioned after it declared that bomb alerts on two Scandinavian airlines SAS planes from Oslo and Stockholm were false.
The two planes landed safely in Brussels on Wednesday and searches of the aircraft turned up nothing.
Belgium has been on high alert since suicide bombers struck Brussels airport and a metro station near the European Union headquarters on March 22, killing 32 people.
A Belgian policewoman last Saturday shot and killed a machete-wielding Algerian man who wounded two female colleagues in the city of Charleroi, authorities said.
IS, also called Daesh, ISIS or ISIL, claimed responsibility for the attack by the man who officials said had been living illegally in Belgium.
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