The 63-year-old, who has rejected numerous calls to stand down as the Republican nominee, is now likely to face increased pressure over his position.
Fillon has been heavily criticized for failing to quit the race since becoming embroiled in a parliamentary scandal over claims that he paid his wife and children for work they did not do.
Tuesday's announcement, by the National Financial Prosecutor, caps a troubling few days for Fillon. He was forced to apologize for an anti-Semitic tweet
sent out by his party earlier this week, and the Journal du Dimanche newspaper alleged that he received a number expensive suits worth thousands of euros from a mystery benefactor.
It said he had received almost 50,000 euros worth of suits and clothing since 2012.
Fillon, who is struggling to make the second round of the French election, has fallen well behind centrist candidate Emmanuel Macron and National Front leader Marine Le Pen in the latest polls.
French voters go to the polls on April 23 but if no candidate gets more than 50% of the vote, there will be a runoff election on May 7.
How did we get here?
Fillon's problems began when French newspaper Le Canard Enchainé published
reports that his wife and and two of his adult children earned nearly 1 million euros ($1.08 million) as parliamentary assistants but didn't show up for work.
But Fillon has rejected the claims and insists that he has "nothing to hide."
He has said his wife worked for 15 years
, as his "deputy," carrying out several roles, including managing his schedule and representing him at cultural events.
Fillon, who was prime minister from 2007 to 2012, said that his daughter and son were employed in similar positions for 15 months and six months respectively, which he said is not illegal, but was an "error of judgment."
The past week has brought new controversies including the Republican party tweeting an anti-Semitic image depicting Macron.
The image was later deleted and Fillon condemned it, tweeting: "I will not tolerate my party using caricatures that use the themes of anti-Semitic propaganda."
On Sunday, he was then forced to defend himself against the allegations he had received suits from an anonymous benefactor.
Fillon has remained defiant so far and has consistently refused to stand down.
Earlier this month he survived calls to step aside with a number of party members reported to have created a "respectful exit plan" for Fillon.
He held a rally in Paris where thousands of supporters flocked to hear him reject calls for him to step aside once again.
That came after former Prime Minister Alain Juppe said he would not be interested in replacing Fillon as the party's candidate.
Fillon, who apologized for the affair, has constantly spoken out against what he perceives as "incredible violence which has never been seen in the Fifth Republic."
His wife, Penelope, has also spoken out against those spreading "crazy rumors" while insisting her husband would "go on until the end" in his bid for the presidency.
But Fillon is not alone when it comes to problems with the law.
Le Pen is also under scrutiny after several members of her staff were accused by officials of being paid for non-existent jobs at the European Parliament.
She initially admitted they had been paid while not working, the European Anti-Fraud Office (OLAF) said. She later denied having said so.
Le Pen's fractious relationship with Europe was further exacerbated when MEPs voted to rescind her parliamentary immunity over a case involving violent images she posted on Twitter.
An inquiry was opened under a French law banning the distribution of violent images, after Le Pen tweeted images of killings by ISIS militants in December 2015.