Prosecutor's spokeswoman Ine Van Wymersch said a car broke through fences at about 02:00 (00:00 GMT).
She said there was "sensitive material" inside the laboratories, but it is not yet clear what if anything was destroyed in the fire.
Five people arrested nearby were later released without charge.
Initial reports in Belgian media said a bomb had exploded. But Ms Van Wymersch said that while a bomb was unlikely to have detonated, it was impossible to fully rule out that scenario.
"The location was not chosen randomly," she said. "It's an important site, that includes sensitive documents relating to current investigations."
"The possibility of a terrorist act is not confirmed. It goes without  saying that several individuals may have wanted to destroy evidence related to  their legal cases," Ms Van Wymersch added.
The case was being treated as arson, she said.
Some 30 firefighters helped put out the fire at the National Institute of Criminology, which Ms Van Wymersch said caused damage but caused no casualties.
Forensic analysis linked to criminal cases is carried out at the site, but while it is not the only laboratory of its kind linked to the police, it is the most important forensic test centre in Belgium.
Images submitted to broadcaster RTL by nearby residents showed flames and heavy smoke rising into the night sky.
The independent institute, linked to Belgium's federal justice body, is in Neder-Over-Heembeek, a suburb in the north of Brussels.
Belgium's terror alert level remains high since bomb attacks on Brussels airport and the city's metro, claimed by so-called Islamic State, that killed 32 people in March.
Attackers rammed a car through the gates of a Brussels crime laboratory before starting a fire to destroy forensic evidence, prosecutors say.