The EU inquiry focused on the role of an assistant, Christopher Adams, who was engaged to work with the Member of European Parliament (MEP).
"Parliament pays salaries to assistants of lawmakers for work directly related to their European mandate", a European Parliament spokeswoman said.
A snap ComRes poll carried out yesterday in the wake of Mr Farage's remarks found that 51 per cent of voters do not want the contest re-run.
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Website Votewatch Europe listed Farage 748th out of 751 MEPs for voting participation at the European Parliament. Mr Adams was Ukip's national nominating officer and was described as one of its "key people".
A source in the European parliament told the Guardian: "Since 1 January  the European parliament has withheld 50% in order to recoup the €40,000 due in salary that was paid to Christopher Adams and which can not be proved by Farage".
Docking Farage's pre-tax MEP salary of €8,484 a month would mean he would have repaid what officials call his "debt to the EU" by October 2018. Farage's pension is understood to be worth £73,000 a year and he will also be entitled to a transitional allowance worth £117,000 when he steps down as an MEP in 2019, as the United Kingdom leaves the EU.
Mr Helmer denied any wrongdoing but gave no explanation as to why he was stepping down.
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For now, they will rely on their partners Lenovo , LG, JBL , and Sony to produce the displays . The displays are powered by a Qualcomm Snapdragon 624 microprocessor.
Two investigations were closed without any formal action.
An Efdd Group spokesman said: "There is a vindictive campaign by the European Parliament of selective persecution of Eurosceptic MEPs, parties and groups". They dismissed the salary cut as a "politically-motivated assault".
Mr Farage has been an MEP for South East England since 1999.
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Helen Whately, MP for Faversham and Mid Kent, said: "I was really surprised to hear Nigel Farage calling for a second referendum".