A man armed with a Kalashnikov was shot dead and four officers were wounded during March 15operation in the suburb of Forest, an official said.
The Belgian capital has since been on high alert, with police said to be searching for suspects who may have fled the raid.
The November attacks in Paris – involving militants from Brussels – left 130 people dead.
ISIS has said it carried out the attacks.
French police also took part in March 15 operation in Brussels. One of the officers wounded in the raid was a French policewoman, officials said.
Police went to search an apartment in the southern suburb of Forest on March 15.
“During this operation, one or several people opened fire on the police as they came through the door,” the federal prosecutor’s office said.
Three officers were injured then and a fourth in a later exchange of gunfire, it said.
“A suspect armed with a Kalashnikov” was also killed at around 18:00 in the street outside the flat, the prosecutors’ statement said.
The Associated Press news agency quotes prosecutor Eric Van der Sypt as saying that several people fled the scene when the gunshots first rang out, and it was not yet clear if all were bystanders, or if some were suspects.
Belgian media reports say police are searching for two more suspects after the raid.
The dead man has not yet been identified. However, a prosecutor’s spokesman had earlier made clear it was not Salah Abdeslam – one of two suspects still on the run after the November 13 attacks in Paris.
French police sources had said earlier that he was not the target of March 15 raid.
Belgium’s De Standaard newspaper quotes its sources as saying that investigators had been expecting to raid a safe house used in connection with the Paris attacks.
They had not expected the flat to be occupied, as its water and electricity had been disconnected for some time.
The operation brought life to a standstill in the area, close to railway lines used by high-speed trains to London and Paris.
Two local schools and two kindergartens were in lockdown for several hours before being evacuated by police.
The prosecutor’s office said the investigation is “actively continuing, day and night” but gave no other details.
Since the November 13 attacks, officials have identified most of the people they believe to have carried out the assaults.
Most of the suspects either died during the attacks or were killed in later police raids.
In addition, 11 people have been arrested and charged in Belgium in connection with the killings. Another eight are still in detention.
Parts of Brussels were sealed off for days after the Paris massacre amid fears of a major incident. A number of suspected attackers lived in the Belgian capital. Police have also carried out a series of raids in the city.
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