"Because of a technical failure with air traffic control no departures or landings are possible at Brussels Airport till 14H00. This is a nationwide problem," Brussels airport authorities said in a statement.
Planes headed to the EU capital were being diverted to regional airports, in an effort to clear Belgium's airspace, airport authorities said.
Planes overflying Belgium however were not affected, authorities said.
Traffic was suspended at the regional airport of Charleroi, a low-cost airline hub near the French border, as well as Liege, near Germany.
Several of the flights were being diverted to Lille airport in France, a spokesman there said. About 1,000 passengers were to travel on from Lille to their intended destination by bus.
About 600 flights a day arrive or depart from Brussels airport.