Railway executive Florence Parly was named France's new defence minister on Wednesday after her predecessor and two other allies of President Emmanuel Macron's centrist party quit amid a party funding investigation.
And two days ago, Richard Ferrand, a junior minister from Macron's En Marche party, also left his government post - his resignation was made at the president's request, after Ferrand became embroiled in a conflict of interest scandal involving his wife.
"This is why I asked the President, in agreement with the Prime Minister, not to be part of the government anymore".
A veteran centrist figure who ran three times for president himself, 66-year-old Bayrou was a key backer of Macron's 14-month-old Republic on the Move (REM) movement, and his support was crucial in lending legitimacy to the inexperienced candidate.
Earlier this year, another preliminary investigation was opened after an MEP from the far-right National Front (FN) party had written to judges to tell them that Modem MEPs were paying party members with European Union money.
Under a government reshuffle to be conducted this week after Macron's party won a majority in parliament at the weekend, Ferrand is to step down as minister for territorial planning. His European Affairs Minister, Marielle de Sarnez, is said to be the next in line.
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Bayrou on Tuesday declared he would not be leaving but by Wednesday morning he had changed his mind and said he would not be in the new cabinet, due to be unveiled later in the day.
The departure of Ferrand, a close friend of Macron, was sold as a promotion; he will lead the REM parliamentary group. "It is a major government crisis", said Laurent Wauquiez, a leader in the conservative Republicans party.
Her own party has been investigated over similar accusations of misusing European Parliament funds to pay for staff in France.
During his campaign, Macron said cleaning up French politics would be one of his priorities.
A preliminary investigation was launched in Paris earlier this month after a former assistant to former MEP Jean-Luc Benhamias told judges that he had been employed mainly for party activities.
In the past 48 hours, four government ministers have resigned from Macron's administration following allegations of corruption.