PARIS — The timing couldn’t have been worse. On the day he presented his bill to “restore confidence” in the political system to the weekly French cabinet meeting, Justice Minister François Bayrou faced new allegations that he and his allies funneled European Parliament funds to help finance his political party.

As if that wasn’t enough, Bayrou’s defiant reply to Prime Minister Édouard Philippe, who had urged him not to call reporters to protest about their coverage of the scandal, has the potential to trigger the first political crisis of the Emmanuel Macron era.

The Bayrou affair presents two delicate problems for the new president. First, his campaign to clean up the system has been tarred by allegations that some of his own ministers may have dirtied their hands in the old games of French politics.

Second, Bayrou’s attitude towards his formal boss Philippe raises questions about his ability to “be a team player,” as noted Wednesday morning on French radio by Christophe Castaner, the junior minister who serves as government spokesman.

The Paris prosecutor last week opened a preliminary probe to try to determine whether Modem, the centrist party Bayrou created in 2007, illegally used work done by assistants to its MEPs in Brussels to benefit the French party’s operations in Paris.

“When you’re a minister, you can’t react as if you were still an ordinary citizen” —French Prime Minister Édouard Philippe

And this week, satirical weekly Canard Enchainé wrote that Bayrou’s own personal assistant Karine Aouadj saw her work contract changed to put her on the European Parliament payroll when Modem went through difficult times back in 2010. Aouadj was made a part-time assistant to then-MEP Marielle de Sarnez, who is now Macron’s junior minister for European affairs. But according to Canard, Aouadj kept working full-time as Bayrou’s assistant.

Bayrou has protested that jobs “never existed” in his party, and insists that, as justice minister, he doesn’t want to comment further on a matter that is now for the French judiciary to decide.

But while Bayrou has pledged to respect French judges and prosecutors’ independence, he hasn’t shown the same resolve concerning the media. He called an editor at a French state-owned radio last week to complain about reporters investigating the matter.

That prompted a stern rebuke from Philippe, who said that he didn’t think “it was a good thing for a minister to ring a journalist.”

“When you’re a minister, you can’t react as if you were still an ordinary citizen,” he added.

Bayrou’s reply to the prime minister, in a nutshell: get lost.

“Every time I will have something to say, I will say it,” he replied a few hours later during a trip to northern France. And the justice minister seemed to double down in an interview with Le Monde on Wednesday: “I have not become mum when entering this ministry,” he insisted. “I will not gag myself.”

Macron has maintained a deafening silence since the scandal-cum-catfight erupted. That is in line with his attitude ever since he was inaugurated a month ago: pose as the above-the-fray president who doesn’t descend to the lower levels of politicking, which are happily delegated to Prime Minister Philippe.

But Bayrou, a seasoned politician who helped propel Macron to the Élysée Palace when he decided to support his presidential bid in February, has the potential to become a lasting political thorn if he keeps behaving as a kingmaker who doesn’t recognize the prime minister’s authority.

A swift decision to dismiss Bayrou would now be easier for Macron to take, because his political party La République En Marche (LRM) is on track to gain an overwhelming majority of seats in the National Assembly, the lower house of Parliament, in the second round of the parliamentary election on Sunday. According to all estimates, Macron won’t depend on Bayrou and Modem for his political future.

The president sent the message on Wednesday that he wanted an end to the Philippe-Bayrou skirmish. While denying there were “particular tensions” between the two men, Castaner, the government spokesman, insisted right after the cabinet meeting that any “attempt to influence the media” on the part of a minister would be “bad for the functioning of democracy.”

“That’s an absolute principle,” he added.

But even if Macron manages to solve the problem of his prime minister’s authority, he will still be faced with the delicate matter of having quite a few of his own ministers subjected to preliminary probes by prosecutors.

Before Bayrou, there was the case of Richard Ferrand, the LRM leader and old Macron associate, now the regions minister, who is facing nepotism allegations dating back to before he became an MP.

So far, the official Macron position on all those cases — as often repeated by both Philippe and Castaner — is that any minister put under a formal (as opposed to preliminary) probe by investigative judges would have to resign, even if he or she would still be considered innocent at that stage.

The cases of Ferrand and Bayrou are different from each other — the former doesn’t deny the facts but said he did nothing wrong, whereas the latter altogether denies the allegations against him and his party.

Still, coming from a president eager to look “whiter than white” on ethical questions, a former Macron campaign aide noted, it may look a bit like a “hypocritical cop-out” to leave such major political decisions to judges.

On the other hand, the aide noted, “Macron wants to look like he’s resisting what he sees as unfair media campaigns. If he starts firing ministers at the first publication of wrongdoing allegations, he won’t have much of a government left to work with.”

PIERRE BRIANÇON