Half of his salary has been withheld to recoup the money the Parliament says it is owed.
The move was condemned by a spokesman for the European Parliament group which Mr Farage heads.
“There is a vindictive campaign by the European Parliament of selective persecution of Eurosceptic MEPs, parties and groups,” said the spokesman for the European Freedom and Direct Democracy group.
“This allegation is all part of their politically motivated assault.”
European Parliament auditors last year suspended the contract of Christopher Adams, who was hired to be Mr Farage’s assistant in Brussels and Strasbourg.
The European Parliament has declined to comment.
The monthly pre-tax salary for an MEP is 8,484 euros (£7,530), which is the equivalent of an annual gross salary, before tax, of 101,808 euros (£90,235). They also receive thousands more in expenses for staff and travel costs.
Mr Farage, who will lose his job as an MEP in 2019 after 20 years in the European Parliament, recently described himself as “skint” in an interview with Mail on Sunday.
The 53-year-old will be entitled to annual EU pension of £73,000 when he reaches the age of 63.
He denied claims of hypocrisy – after campaigning for Brexit – saying: “Why should my family suffer?”
“I have just voted to get rid of my job. I was the turkey that voted for Christmas. How is that hypocrisy?,” he told the BBC’s Andrew Marr show.
He added that he doubted the money, which would be partly funded by money from the so-called EU divorce bill, would ever be paid, saying: “Given the arbitrary way the European Union behaves in terms of money, I would be very surprised if I get any of it. I don’t think it will even occur.”
A 2016 investigation by the European Parliament alleged funds for the EFDD group – which includes UKIP and other Eurosceptic parties – had been wrongly spent “for the benefit of UKIP”.
It said the group should repay £146,696 of the funds intended for European Parliament business.
An Electoral Commission investigation into whether the party broke UK electoral law is ongoing.