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."
Galant said the leak was part of a vendetta against her by a disgruntled senior transport official and insisted that she always 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.
Galant says she had not seen the EU report but Michel said "a summary of this report was discussed and sent to the minister's cabinet in June 2015."
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No immediate replacement was named for Galant but Michel said he would do so as soon as possible.
The suicide attacks in the peak morning travel period have shaken the Belgian government, police and judiciary. The Belgian parliament has set up an inquiry to look into any shortcomings in the handling of the bombings. Belgium's interior and justice ministers volunteered to step down last month, but their resignations were rejected.
At a hastily organised press conference, a defiant Galant rejected allegations that she had been lax about security. "If there's an area I always paid attention to it's that one," she said.
She told reporters she is the victim of a "media crusade" organised by a senior transport official whose attacks on her would not end until she resigned. Galant accused her foes of "riding the current wave of worry" provoked by the Brussels attacks.