Le Pen had been summoned previously in court, but refused to go during her campaign bid for the French presidency.
Investigators suspect the FN used money from Brussels earmarked for parliamentary assistants to pay staff to work for the party in France.
Le Pen has already had her parliamentary immunity lifted over a separate case from 2015 when she shared graphic pictures of atrocities committed by the Islamic State group on her Twitter account.
The fake jobs scandal implicating Le Pen started with an expenses inquiry in which the European Parliament first accused her far-right National Front party of defrauding it to the tune of some Euro 340,000 (USD 360,000).
Ms Le Pen ran for president in France's May election, on an anti-immigration, anti-EU platform.
In a statement, her lawyer said she would launch an appeal.
Le Pen, a former member of the European Parliament, was charged with breach of trust for allegedly placing her chief of staff and her body guard on the EU payroll between 2009 and 2016. Three of his ministers bowed out of their jobs shortly after being appointed - the justice, defense and European affairs ministers - over concerns they could be caught in the investigations into the political use of salaries to parliamentary aides.
The charges filed against Ms Le Pen, who is not accused of trying to enrich herself personally, are preliminary and mean only that the judges working on the case have suspicions that are strong enough to formally place her under investigation.
She was elected to the French parliament this month so gave up her seat in the European Parliament.
If tried and convicted, Le Pen faces up to three years imprisonment and a fine of up to Euro 375,000 (USD 425,000), although it is unlikely she would receive a custodial sentence.
At Friday's meeting with the magistrates, she read out a declaration and declined to answer questions, as allowed by the law, her lawyer told AFP.