A confidential document shows security lapses at Belgium’s airports were identified by EU inspectors in 2015.
Jacqueline Galant had denied having seen the report, which was leaked by opposition parties.
ISIS attacks on Zaventem airport and a Brussels metro station left 32 people dead.
Belgian PM Charles Michel had previously defended Jacqueline Galant, and he had told parliament that her office had not seen the critical EU report.
However, on April 15, following the publication of further documents on April 14, Charles Michel said that “contrary to what was communicated to me” the report had been discussed, according to public broadcaster RTBF.
Charles Michel said he had met Jacqueline Galant on April 15 and following the meeting the minister submitted her resignation to the king.
Jacqueline Galant wrote in her resignation letter that “the orchestrated and theatrical confusion of the last 48 hours prevents me from continuing in the performance of my duties”.
The minister’s resignation followed that of Belgian federal transport agency chief Laurent Ledoux on April 14.
Laurent Ledoux had complained of a lack of funding from Jacqueline Galant and said that the minister herself should “take responsibility and step aside”.
Jacqueline Galant said on April 15 that she was shocked by the way Laurent Ledoux had resigned, and said he was carrying out a “media crusade”.
The 2015 European Commission report, published by public broadcaster RTBF, cited “serious deficiencies” and said airport security programs, air carriers and suppliers were “not adequately monitored”.
The two suicide bombers who attacked Brussels airport blew themselves up in the departures area and would not normally have faced any security checks.
The bomb attacks on the airport and Maelbeek metro station occurred just four days after Paris attacks suspect Salah Abdeslam was caught near his home in Molenbeek. He had been on the run for four months.
Belgium’s parliament is to hold an inquiry into how the attacks were handled.
The interior and justice ministers both offered to resign in the immediate aftermath of the attacks, following revelations that Turkey had warned Belgian authorities about one of the attackers when it deported him back to Belgium, but the prime minister asked them to stay on.
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