The affair is the lone snag in an otherwise trouble-free start to Macron's tenure.
For days, France's new government has been swatting away allegations that Richard Ferrand, one of Macron's first prominent backers, favoured his wife in a lucrative deal with a public health insurance fund when he headed the company.
The affair is the lone snag in an otherwise trouble-free start to Macron's tenure, during which he has been praised for standing up to US President Donald Trump and taking a firm line with Russian leader Vladimir Putin.
Ferrand, a former Socialist lawmaker who joined Macron's camp last year and helped run his campaign, has persistently denied any wrongdoing and rebuffed calls by rivals for his resignation.
"I am an honest man," the 54-year-old minister for territorial cohesion told France Inter radio on Wednesday.
The investigative Canard Enchaine newspaper reported last week that an insurance fund that Ferrand headed in his native Brittany -- where he is an MP -- agreed in 2011 to rent a building from his wife and carry out renovations that boosted its value.
Ferrand has dismissed the report as a "welcome present" from the media for the new government, saying his wife made the fund the best offer and that he had no say in the matter.
The revelations are nonetheless an embarrassment for 39-year-old Macron who campaigned on a promise to clean up and rejuvenate France's corruption-plagued political class.
His first piece of legislation -- to be unveiled next month -- will set new standards for ethics in public office.
Addressing a cabinet meeting Wednesday, Macron stressed the need for ministerial "exemplarity" but also urged the media to reserve judgement.
"All is not well when the media acts as judge," government spokesman Christophe Castaner quoted him as saying.
The Ferrand affair, as it has been dubbed, is an unwelcome distraction for Macron in the run-up to June parliamentary elections.
The crusading centrist badly needs to score a majority to push through his ambitious labour and economic reforms.
Prime Minister Edouard Philippe on Tuesday said he understood the "exasperation of the French" faced with a steady drip of political scandals but stressed Ferrand would only be forced to resign if formally charged.
Prosecutors have said they currently have no grounds to do so, saying Ferrand is not accused of doing anything illegal.
French media warned however that the affair risked tarnishing Macron.
On Tuesday, another of his ministers was thrust into the spotlight after being accused by the far-right National Front of misusing European Parliament funds.
European affairs minister Marielle de Sarnez has filed a complaint for slander.
"Do what I say, not what I do," the left-wing Liberation daily wrote in a biting front-page headline Wednesday, alongside a picture of Ferrand. It added in an editorial: "When you preach morals in public life, this is a messy affair."