Bayrou's resignation comes hours before President Emmanuel Macron reshuffles his government, BBC reported.
The minister's centrist party MoDem, allied to Macron's La R?publique en Marche party, is facing an inquiry into claims that it used EU funds to pay party workers.
MoDem has lost all three posts in Macron's cabinet within 24 hours. Defence Minister and former member of European Parliament Sylvie Goulard was the first MoDem minister to hand in her resignation on Tuesday.
After Bayrou said he was standing down, it became clear that European Affairs Minister Marielle de Sarnez was also leaving the government to take over as head of MoDem in the National Assembly, the report said.
Macron's close ally Richard Ferrand also stepped down on Monday amid allegations that he had used insider information to secure a property deal for his wife while he was head of a mutual health insurance fund.
Ferrand and Goulard denied any wrongdoing. Bayrou said he will hold a press conference later in the day at 5 p.m.
(This story has not been edited by Social News XYZ staff and is auto-generated from a syndicated feed.)
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