Police had earlier surrounded an apartment after four armed men took a captive in a working-class area of the northwestern city.
The three suspects were "taken outside, with their hands in the air" by special armed police, Flemish-speaking VRT public television reported, while the fate of the fourth man was unclear and the situation was continuing.
Neighbours said the occupants of the apartment were "drug traffickers", but Belgian authorities would only confirm that they suspected it was an isolated incident with no terror links.
"There is no indication that this is linked to terrorism, the Islamic State or what is happening at the moment in Sydney," the Ghent prosecutor's office told AFP.
The Belgian siege happened at the same time as a lone gunman kept terrified staff and customers captive in a cafe in Australia's largest city, brandishing an Islamic flag.

Latest News from World News Desk