The strike, called by three unions, severely disrupted the country's public transport, particularly in Brussels, where a meeting of NATO ministers was set to take place.
The national railway company expected half the trains nation-wide would be cancelled because of the movement, but high speed train traffic to London and Paris should be mostly spared.
The air traffic control agency, Skeyes, announced on Tuesday that it would not allow any flights to or from the country because it could not determine with certainty which employees would come to work.
No aircraft flying below 8,000 meters altitude would be allowed to fly over the country, the agency warned.
Skeyes was not able to say how many flights or how many passengers would be affected.
Unions are calling for higher wages, putting pressure on the right-of-center government ahead of general elections in May.
Brussels, home to NATO, will be hosting a meeting of defense ministers that day, with officials from throughout the transatlantic military alliance converging on the city.
"We have no indication of any impact of the strike on the meeting," a NATO official told AFP.
Charleroi airport, the second largest in Belgium and a local hub for low-cost giant Ryanair, had already announced its closure.
Belgium's Brussels Airlines has cancelled all its 222 flights.
The German carrier TUI fly will operate its scheduled Belgian flights from the nearest French and Dutch airports.