Prime minister Charles Michel said after his talks with transport minister Jacqueline Galant, “the minister presented her resignation to the King and the King accepted it”.
Ms Galant said the leak was part of a vendetta against her by a disgruntled senior transport official and insisted she paid very close attention to security concerns.
The confidential EU document from last year was made public by two Belgian opposition parties. It called the oversight of security measures at the nation’s airports flawed and cited serious deficiencies in the way safety checks were managed.
The revelations came after the March 22 attacks in Brussels killed 32 people, including 16 at the national airport, and left 270 people wounded. IS has claimed responsibility for the attacks.
Ms Galant says she had not seen the EU report but Mr Michel said “a summary of this report was discussed and sent to the minister’s cabinet in June 2015.”
Mr Michel said he would name Ms Galant’s replacement as soon as possible.
The Belgian parliament has set up an inquiry into any shortcomings in handling the bombings. Belgium’s interior and justice ministers volunteered to step down last month, but their resignations were rejected.