The dead person had not been identified but prosecutors said it was not Salah Abdeslam, a key suspect in the November Paris massacre which killed 130 people, and who fled to Brussels after the attacks.
Armed police came under fire as they carried out a search on a property in the Forest suburb in the south of the Belgian capital, sparking a series of gun battles in which one suspect was killed, prosecutors said.
"A body was found during a search of a house ... His identity has not been established yet but whatever the case, it is not Salah Abdeslam," Van Der Sypt was later quoted as saying by the Belga news agency.
Three Belgian police officers were wounded by gunfire during the initial search of the property, while a fourth was hit by gunfire during the huge police mobilisation afterwards.
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Dozens of security forces in balaclavas armed with submachine guns cordoned off the scene, while police vehicles with flashing lights rushed into the search area, AFP reporters said.
The local mayor said that two people were believed to be holed up in a house, but as the operation appeared to be winding down, authorities later only mentioned the suspect who was killed, without saying if they were searching for more.
French Interior Minister Bernard Cazeneuve confirmed earlier that French police were also involved and said the attackers used assault rifles.
"A team made up of Belgian and French police came under fire, apparently from assault weapons, during a raid," he said after arriving in the Ivory Coast capital following a weekend shooting rampage by jihadists there that killed 18.
Parents at the cordon line became increasingly distressed as they were unable to get to their children, before they were eventually let out one by one, accompanied by armed police.
Police also started letting people back into their homes.
The incident took place across the street from an Audi auto factory and the train lines leading to the Gare du Midi railway station from where Eurostar trains run to London and Thalys trains to Paris.