Belgium's transport minister resigned on Friday after being accused of ignoring damning EU reports on the poor state of security at the country's airports that was laid bare by last month's suicide attacks.

"Transport Minister Jacqueline Galant has offered her resignation to the king, which was accepted," Prime Minister Charles Michel said after a cabinet meeting, according to a statement from the royal palace.

Galant was under fire after the EU reports were leaked to media and following the shock resignation of a top transport official who accused her of incompetence and "Gestapo-like" behaviour.

Two Islamic State attackers blew themselves up in the departure hall at Brussels airport on March 22 in a first wave of coordinated attacks that also hit a Brussels metro station, killing a total of 32 people. 

The EU reports only pertained to areas of the airport beyond security checks, but they pointed to "serious deficiencies" in security including the tracing of explosive devices.

The latest report from 2015 said Belgium was still "non-compliant, with serious deficiencies" in five areas and "non-compliant" in three areas based on a visit to Antwerp airport.

Galant denied she was ever made aware of the reports that also said the relevant authorities were woefully understaffed.

But a top official said he had clearly notified Galant and her office on the matter.

Galant was also responsible for Belgium's embattled air traffic control authority which was subject to strike action this week that caused hundreds of cancelled flights.

The European Commission, the EU regulator that drew up the report, declined immediate  comment.