The move comes a week after the prosecutor said the matter could not be dropped, because the office had received a police report.
The allegations started when Le Canard Enchainé newspaper published reports that Fillon's 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.
The 62-year-old 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."
He did offer an apology to the French people on February 6.
His lawyer, Antonin Levy, accused the prosecutor's office of failing to prove any wrongdoing in its initial inquiry,
which he described as "unacceptable" just a few weeks before a presidential election, scheduled for April 23.
The investigation will look at allegations of embezzlement of public funds, misuse of public assets, complicity and concealment of such objects, traffic of influence and noncompliance with the reporting obligations before the High Authority, according to the financial prosecutor's office.
Effect on presidential elections
Fillon became the Republican parties nominee in November and is a leading contender in the presidential race, where he faces stiff competition from independent candidate Emmanuel Macron and far-right National Front candidate Marine Le Pen. The French Socialists nominated Benoit Hamon.
Le Pen's campaign was embroiled in controversy this week
after her chief of staff was hit with a formal judicial investigation into whether she held a fake European Parliament job.
Catherine Griset and Le Pen's bodyguard, Thierry Legier, are alleged to have been paid for non-existent jobs at the European Parliament.
If neither candidate gets more than 50% of the vote in the balloting on April, 23, there'll be a runoff on May 7.