“The identity of the person is known and (they are) being actively pursued,” the official said, adding it was someone from the area.
The presumed assailant abandoned his vehicle nearby.
An AFP journalist at the scene said a military bomb squad had arrived on the site as well as a SWAT team.
The perimeter has been sealed off by police, with a helicopter flying overhead, he said.
Officials told AFP no immediate motive for the attack was known and there was so far no report of any casualties.
The Flawinne base in the central Belgian city is home to a commando battalion of 650 soldiers that participate in NATO operations and peacekeeping missions.
The incident stirred memories of recent deadly attacks, including the killing of four people at the Jewish museum in central Brussels in 2014 by a jihadist gunman.
In January, the security forces killed two suspected jihadist fighters in Verviers, eastern Belgium, who they said were planning imminent attacks.