Le Pen is one of 17 European Politicians in the National Front being investigated in relation to this fraud, including Le Pen's own father Jean-Marie Le Pen.
Sixteen other National Front representatives in the European Parliament have been under investigation by the French authorities since 2015.
Later the cost was estimated at Euro 1.9 million but the new estimate cited by police sources is more than twice as high - Euro 4,978,122.
The European Parliament believes the money went to National Front employees working for the party in France rather than those working for its lawmakers in Brussels.
In March, French investigators raided the party's headquarters outside Paris in order to find out if the European Parliament funding for MEP assistance had been abused with fake jobs.
The probe and looming possibility of a trial for Ms Le Pen come at a hard time for her party, which was thrown into turmoil by her loss in the presidential race and its lacklustre showing in the legislative elections that followed.
France's Marine Le Pen charged over funding scandal
On Monday, Le Pen is to appeal the investigating magistrates' decision which "violates the principle of the separation of powers", according to the defense lawyer, Xinhua news agency reported. Her bodyguard was also questioned but was later released without being placed under investigation.
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.
At the time, Le Pen was competing closely with ultimate victor Macron.
The French judiciary has already requested that the European Parliament lift Le Pen's immunity. She was also charged for being complicit in the whole party's breach of trust, as the party leader.
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. She had however promised to cooperate with the investigation after the May presidential and June parliamentary elections were over.
Le Pen was first elected to the European Parliament in 2004.
"It makes no sense", National Front vice president Florian Philippot, Le Pen's top lieutenant, said on the BFM-TV station.