Police said the 26-year-old was wounded in the leg in the operation, which took place as EU leaders met on the other side of the city to discuss Europe’s migration crisis.
Several exchanges of gunfire rang out in the Molenbeek area – the scene of past investigations into the Paris attacks – and police officers were seen surrounding an apartment block there.
There were unconfirmed reports that two people had been arrested and that a third suspect may have been involved.
The police operation in Molenbeek was launched just as Belgian prosecutors confirmed that Abdeslam’s fingerprints had been found at a flat that was raided in the Forest area of Brussels on Tuesday. Two suspects fled that raid.
Abdeslam, a 26-year-old French national who grew up in Brussels, fled Paris for Belgium by car hours after the 13 November attacks that killed 130 people.
Police believe he played a key role in the logistics of the Paris attacks and escorted the three suicide bombers who blew themselves up at the Stade de France as part of the coordinated assault.
Investigators are also considering whether he planned to carry out his own suicide attack in the 18th arrondissement of the French capital, and perhaps backed out. His brother blew himself up and died at a Paris bar on Boulevard Voltaire during the attacks.