According to the rules, MEPs cannot vote on behalf of another MEP.
The accusations are the latest in a series of controversies involving the right-wing politician in recent months. Last week she appeared in court accused of inciting racial hatred.
She denied committing any offence when she compared Muslims praying in the street to the Nazi occupation.
In the latest scandal on Wednesday, the vice president of her political group is alleged to have voted for himself as well as for Ms Le Pen at least eight times.
"She just got up and left in the middle of the voting session, and you can clearly see National Front Vice President Marcel de Graaff voting for her," parliament spokeswoman Marjory Van Den Broeke told the BBC.
Manfred Weber, leader of the EPP group in parliament. said that in the light of the accusations, he will send a letter to European Parliament President Martin Schulz, asking him to open a formal investigation into matter.
Mr Schulz`s office told the BBC that he is looking into the allegations.
He has the power to sanction MEPs by suspending them, fining them, or cutting their daily allowance.
But Ms Le Pen is quoted by French media as saying that even if there was a breach of parliamentary procedures, Mr de Graff will have to take responsibility for it rather than her.
Her anti-immigration and anti-EU message is attracting increasing support in France and her party is hoping to win two French regions in December`s local elections.
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