Some 200 of 400 scheduled flights were cancelled, an airport spokeswoman said. One of Europe's busiest, Brussels airport had reopened 10 days ago at much reduced capacity following the Islamic State attacks on March 22.
Air traffic agency Belgocontrol said it was still trying to resolve the dispute with a union that represents about 80 of 280 staff over plans to raise their pension age from 55 to 58. The economy minister said other unions asked their members to fill in for colleagues who have been calling in sick as a protest.
IATA, the international airlines association, called their action a "kick in the teeth" for them and for airport staff who have worked speedily to replace the bomb-ravaged departure hall and restore connections to the EU's capital city.
Irish carrier Ryanair said it would sue for damages.
As government ministers weighed in to seek a resolution, some Belgian media condemned the striking controllers as selfish and pampered. Other commentators lamented the further blow to Belgium's image after criticism of its failures to prevent local militants attacking both Brussels and, in November, Paris.
"This country no longer needs terrorists to blow it up," fumed Le Soir newspaper. "It's doing it all on its own, with its absurdities, its lack of responsibility, its going off in all directions, its pantomimes. Have we lost our sense of reality?"
