The move comes after the deadline passed for Le Pen, France's far-right leader, to return more than €300,000 the Parliament says she has misspent.
Le Pen, a presidential candidate in this year's French elections, had until midnight on Tuesday to repay the money but failed to do so. She said she had no intention of paying.
The Parliament says she wrongly used the funds to pay an aide at the National Front's headquarters in Paris.
But Le Pen says she is the victim of a politically motivated vendetta.
On Wednesday, a spokesperson for Parliament told this website, "The European Parliament accountant has sent a letter to Le Pen this morning saying that as the debt owed to the Parliament has not been repaid, it will now proceed to the recovery of the money by withholding 50 per cent of her salary, 100 per cent of her general expenditure allowance, and 50 per cent of her daily allowance."
The press officer added, "This is an administrative, bookkeeping measure to recover money which was paid out unduly.
"Le Pen has had ample occasions to demonstrate that the assistant concerned did indeed do work strictly linked to the exercise of Le Pen's mandate as a member of the European Parliament."
UK Tory MEP Charles Tannock backed the Parliament, telling Parliament Magazine, "I fully support the right of EU institutions to use all legal means to prevent improper use of EU funds including using of MEP secretarial allowances for fictitious or disallowed use. Therefore all legal means to recover such use of funds is to be welcomed."
The ECR group member added, "No one, even a group President or national Presidential candidate, is exempt from the rules we backbench MEPs have rightfully to observe in an honest and transparent manner."
Le Pen is one of the front-runners in the French presidential election to be held in April and May. If she wins, she has promised a Brexit-style referendum on France's membership of the EU.
Polls suggest that she will make it to the second round of the elections, where she is likely to face conservative candidate Francois Fillon or centrist Emmanuel Macron.
On Tuesday, she told Reuters news agency, "I will not submit to the persecution, a unilateral decision taken by political opponents. without proof and without waiting for a judgement from the court action I have started."
The money the European Parliament wants returned was used to pay the salary of Catherine Griset, a close friend of Le Pen as well as her cabinet director.
The funds were conditional on Griset spending most of her working time in Brussels or Strasbourg.
However, the Parliament says most of her time was instead spent working in the National Front's headquarters in Paris. The party will face a second demand for €41,554 in wages paid to her bodyguard.