Nigel Farage will be docked half his monthly MEP salary
Mr Farage will have to pay back £35,000 to Brussels.
Last year the work contract of Mr Farage’s aide, Christopher Adams, was suspended after he was found to be responsible for selecting Ukip candidates in Britain.
A subsequent investigation by EU parliamentary authorities concluded Mr Farage had diverted EU funds towards national political activities.
The money will be reclaimed by withholding half of his £7,535-a-month MEP salary between January and October.
A spokesman for the European Freedom and Direct Democracy group claimed: “There is a vindictive campaign by the European Parliament of selective persecution of Eurosceptic MEPs, parties and groups.
“This allegation is all part of their politically motivated assault.”
The news comes after Mr Farage earlier this week suggested he wanted a second referendum on the UK’s European Union membership.
Appearing on Channel 5’s The Wright Stuff, he said: “What is for certain is that the Cleggs, the Blairs, the Adonises will never ever ever give up.
“They will go on whinging and whining and moaning all the way through this process.
“So maybe, just maybe, I’m reaching the point of thinking that we should have a second referendum on EU membership… unless you want to have a multiple-choice referendum which would confuse people.
“I think that if we had a second referendum on EU membership we would kill it off for a generation.
“The percentage that would vote to leave next time would be very much bigger than it was last time round.
Nigel Farage will have to pay back £35,000 to Brussels
“And we may just finish the whole thing off. And Blair can disappear off into total obscurity.”
However, the former Ukip leader has since sought to clarify his remarks, arguing while he doesn’t want another vote, a second referendum may be inevitable as the EU will offer Britain such a bad deal it will be rejected by Parliament, and the Government will not leave the union without a deal.
Writing for the Telegraph, Mr Farage said: “To be clear, I do not want a second referendum, but I fear one may be forced upon the country by Parliament. That is how deep my distrust is for career politicians.
“This poses a big question for Leavers. Do we stick with the view that the result will stand or acknowledge the fact that we face this potential threat?”