The investigation for "misuse of public money" was triggered by a report in the Canard Enchaine newspaper, which claimed that British-born Penelope Fillon had been paid from money available to her husband as a longstanding MP for the northern Sarthe region.
Fillon fights back
Fillon sought to fight off a scandal about his wife on Wednesday following a press report that she earned big salaries for work she never did - a charge that could upset his smooth ride into the Elysee.
Fillon, a right-wing former prime minister, said he was outraged at the report.
"I see the stinkbomb season has started," the 62-year-old commented to journalists in the city of Bordeaux.
It is common practice for French parliamentarians to employ wives, children and even mistresses in their office.
But the allegation that Fillon's wife was paid for fake jobs - a charge to which he did not reply directly on Wednesday - could undermine his pledge to pursue an honest and transparent campaign and hurt his ratings as the race for the presidency gathers pace.
Fillon is running for The Republicans party in the presidential election on April 23 and May 7.
While favorite to win election, he faces a strong challenge from the far-right leader Marine Le Pen, second in the polls, and from independent centrist Emmanuel Macron.
That lead could be affected by how Fillon handles a crisis that risks denting his image as a devout Catholic and family man with a relatively scandal-free record in office.
Polls have for months highlighted voter discontent with the political elite and any hint of improper use of public finances could worsen that perception at his expense.
Socialist former prime minister Manuel Valls, who hopes to win his party's ticket as presidential candidate, urged Fillon to explain himself on the matter.
"You can't be the candidate of honesty and transparency and not respond," Valls told France Inter radio.
Le Pen, Fillon's main election foe, usually trades in voter distrust of mainstream leaders but she remained conspicuously silent.
Her own National Front party is under judicial investigation over allegations of improper employment of assistants by its lawmakers in the European Parliament.
"I am not going to get involved in this policy of stinkbombs," she replied when asked on Europe 1 radio. Regarding the inquiry into her own party's finances, she curtly responded: "I am not embarrassed at all. I am the victim of total injustice."
Lifting the lid
Le Canard Enchaine, which has lifted the lid on political shenanigans for decades, reported that Penelope Fillon had been paid 600,000 euros ($644,700) for many years of employment as a parliamentary assistant to him and later to his replacement as a National Assembly lawmaker, and for work at a cultural journal.
It said that its research had showed there was no evidence she had ever really worked.
Fillon's public relations team have emphasized there is nothing illegal about her working for her husband in the National Assembly.
They explained her apparent lack of presence in the work-place by saying she preferred to work "in the background", in keeping with her self-effacing style. They have not said how much she was paid.
Fillon and his wife, who is from Wales, were married in 1980 and have five children.
Last October, she told a newspaper, Le Bien public: "Up to now, I have never been involved in the political life of my husband."
The image conveyed by glossy magazines and television shows is of a woman leading a country life and keeping home for Fillon and their children in their 12th century chateau near Le Mans, west of Paris.
Shortly before he went on to win the conservative nomination in a primary vote last November, Fillon gave a lengthy interview to a TV channel in the elegant gardens of their home.
In that interview, he emphasized the importance of family, saying he would never let politics encroach on his private life.