No planes were allowed to land or take off anywhere for about two hours.
Belgocontrol tweeted that it was imposing a “clear sky” until the glitch was solved.
It said “there is a problem loading flight data” but did not provide further details.
Dominique Dehaene, of Belgocontrol, told the VRT network that “it is a very specific problem and it was no longer sure that all information of flights was correct”.
Eurocontrol, which itself is based near Brussels airport, tweeted: "Problem with the flight data processing system in Belgium's lower airspace (below 24,500 ft/7,500 metres): the regulation has been extended to 17.00UTC (19.00 local time). Currently very few flights in/out of Belgian airports."
Dozens of flights were cancelled, including links to and from Birmingham and Edinburgh.
Shortly after 5pm UK time, Belgocontrol tweeted again to say: "Problem with flight plan data is resolved. Belgian sky totally open again."
The failure happened on one of the busiest days of the year; Friday is expected to see a record number of flights in the skies of Europe.
Last year Brussels international airport saw nearly 25m passengers, while 7.7m passed through Charleroi Airport.
The hubs operate about 650 and 140 flights a day, respectively. Heathrow, Europe's busiest airport, runs about 1,299 a day.
Two years ago another technical problem caused chaos across Belgium. A failure in the country's air traffic control system led to hundreds of flights being cancelled.
More about: Belgium
