Catherine Griset and Le Pen's bodyguard, Thierry Legier, are alleged to have been paid for non-existent jobs at the European Parliament.
Griset was put under formal investigation regarding allegations of concealment of breach of trust. She was released from custody as the judiciary began an investigation on the parliamentary assistants of the far-right National Front, the Paris prosecutor's office said.
It was not clear late Wednesday whether Legier was in custody.
Le Pen, leader of the National Front, initially admitted they had been paid while not working, the European Anti-Fraud Office (OLAF) said. She later denied having said so.
Le Pen was defiant when questioned about the investigation earlier Wednesday on CNN affiliate BFM TV.
"If this situation amuses the magistrates," she said. "The thing I find the most surprising is that an investigating judge is supposed to be taking care of the case. Why is it necessary to lead another inquiry? Because this file is empty.
"The French know exactly how to tell the difference between real affairs and political cabals," she added.
Le Pen, interviewed by broadcaster TF1, questioned the timing of the inquiry.
She said, "the investigation opened two years ago and now, two months before the presidential election there is a search at my headquarters while I am abroad."
The first round of voting this year is on April 23. The runoff is scheduled for May 7.
Le Pen said she was challenging allegations by the European Anti-Fraud Office, which is based in Brussels.
"OLAF is a structure that is not independent from the European Commission," she told TF1. "I filed a complaint with a Belgian lawyer. This institution must not come to disrupt the campaign which is a fundamental democratic moment for the country."
National Front HQ searched
On Monday, the National Front confirmed a search had taken place at its headquarters.
"This is obviously an operation led by the media, whose only aim is to try and impair the proper functioning of the presidential campaign and harm Marine Le Pen's reputation," the party said in a statement.
"This is happening at the very moment when [Le Pen] is significantly gaining voting intentions, notably in the second round."
Le Pen, who has been a member of the European Parliament since 2004, has been asked to pay back a total of €340,000 ($357,000) but is refusing to do so.
In an interview with CNN
earlier this month, she described the issue as a "political attack."
"It's inadmissible. We have been persecuted by the EU Parliament. They are our adversaries," she said, adding that she had filed a complaint against the European Anti-Fraud Office.
Le Pen is fiercely Euroskeptic, and has promised to hold a referendum on France leaving the European Union if she is elected president.
The National Front leader is not the only presidential candidate caught up in a financial scandal. Republican party contender François Fillon
has been accused of paying his wife and children
for work they did not do.
Fillon has rejected the claims and refused to stand down, insisting he has "nothing to hide."