Roger Helmer, a key member of Ukip’s top team, is resigning from the European parliament, ahead of a demand to repay around £100,000 of EU money for alleged misuse of public funds.

The veteran politician, known for his controversial remarks on climate change, rape and homosexuality, is standing down from the European parliament on 31 July, after an 18-year career as an MEP.

He can appeal against the repayment demand at the European court of justice in Luxembourg. If he loses, the parliament has the right to claw back the money by withholding a chunk of a generous “transitional allowance” MEPs get on their departure.

His resignation was announced in a European parliament notice published in Strasbourg on Tuesday. No explanation was given for Helmer’s decision to resign midway through the European parliamentary term.

The Guardian has learnt that Helmer faces a bill close to £100,000 for illicitly employing a Ukip party worker, Paul Oakden, as his assistant. Oakden’s contract has already been suspended.

MEPs are banned from hiring full-time assistants who have jobs in national political parties. Paul Oakden was employed as Helmer’s assistant, while also working as Ukip chairman, according to the party website and in-house magazine.

European parliament financial controllers began their investigation last year and are due to send Helmer a formal “letter for recovery” because they are not satisfied with his explanations of an “administrative misunderstanding”.

Helmer can appeal to the European court of justice in Luxembourg to contest the repayment demand, but if he loses the parliament can claw back the money from a possible €159,000 transitional allowance that the MEP is entitled to for two years after stepping down.

The sum for Helmer’s transitional allowance has been calculated by the Guardian using the parliament’s rulebook, but the final amount could vary and has not been set by in-house accountants.

Contacted by the Guardian, Helmer said: “The only comment I have is how do you know about it and I don’t.”

He declined to answer further questions, but said he would make a statement in a regular news bulletin to his supporters later on Tuesday.

The Guardian was copied into an email Helmer sent to senior officials at the European parliament in February, where he rejected the allegations as “black propaganda”.

Helmer is one of eight Ukip MEPs who has been investigated by European parliament financial controllers for alleged misuse of EU funds in 2017. Investigations are ongoing into the offices of Ukip former leaders Paul Nuttall and Nigel Farage, as well as other MEPs, including Raymond Finch, a Farage protege. The parliament has closed cases into assistants working for James Carver and Jonathan Arnott, without further action. But further demands for repayment of EU funds are expected.

Helmer, 73, was a businessman who was elected to the European parliament in 1999 as a Conservative party MEP and re-elected in 2004 and 2009 before defecting to Ukip in March 2012.

Known for his hostility to climate science, Helmer has described global warming as “myth” and as a Conservative MEP spent public money on a billboard campaign decrying wind turbines in his East Midlands constituency.

He caused outrage when he said some people find same-sex relationships “distasteful if not viscerally repugnant” and argued that there are “different degrees of culpability” in rape cases. Farage, then Ukip leader, said some of Helmer’s remarks on homosexuality had gone too far.

But the MEP continued to play a prominent role in Ukip’s team and was deployed on the airwaves to defend the party, when in 2016 it was asked to repay €173,000 (£148,000) in misspent EU funds and denied an even larger amount in grants, for misspending EU money. A European parliament political group dominated by Ukip was found to have broken EU rules by pouring European money into their campaign war-chest in the 2015 British general election.