Natfhe president Sam Allen has strenuously denied any irregularity over his expenses and may take legal advice after being accused of over-claiming more than pound;1,000 from the union.
The allegation was brought to the attention of Paul Mackney, the lecturers' union's general secretary, after a double payment for pound;726.50 was discovered by the finance office at the headquarters in London.
After being challenged by Fawzi Ibrahim, the union's treasurer, Mr Allen said he mistakenly asked for the payment to be made because he did not notice it going into his bank account the first time round.
Mr Ibrahim has also recovered more than pound;400 from Mr Allen in relation to what he claims are "inappropriate" hotel expenses and claims for taxi fares between his home in Birmingham and the city's New Street Station.
This money is being deducted in instalments from Mr Allen's expenses claims as they come in.
Mr Allen flatly denies over-charging the union and says he will take legal advice to recover the deducted money after his term as president ends in May next year.
He told FE Focus: "I will get through my presidency. Then I will take him (Mr Ibrahim) on. I am too busy at the moment, in discussion with the AUT about merger and other things and promoting the union. I think a lot of this is malicious."
A letter seen from Mr Ibrahim to Mr Mackney seen by FE Focus says: "I think this a matter for you to deal with. I have already made you aware of a series of inappropriate expenses claimed by the president, Sam Allen. These included not just claims for which he is not entitled, but claims that exceeded what Sam actually paid out, such as overnight stays and taxi fares."
Mr Ibrahim checked fares directly with taxi firms in Birmingham, but Mr Allen said any prices which were quoted would not have taken account of city centre congestion, the higher charges from the station taxi rank, or tips.
He said: "Taxis ranged between pound;8, pound;9 and pound;10. Sometimes there's as much as pound;2 on the clock before you are out of the station.
"The highest I have claimed is pound;11. One road into Birmingham was partially blocked as well. Most taxis avoid that."
Mr Mackney says he will not take action unless Mr Ibrahim and Mr Allen are unable to resolve the dispute and stressed he has seen no evidence of fraud.
He said: "I have said to the treasurer 'I think you should present the issues involved to Sam first'."
On the pound;726.50 double payment, Mr Allen says he may have become confused because he has more than one bank account.
He said: "The first cheque was paid into my savings account. The second one went into my current account. Finance office set up a repayment system which I signed and now the money is being paid back to the union.
"It is not a question of Sam Allen trying to get it twice. This has been blown out of all proportion.
"There is nothing I have done which was intended to defraud the union. He (Mr Ibrahim) is not happy about my election. I acted in good faith and have showed them the receipts."
FE Focus reported last year that Mr Ibrahim had turned down Mr Allen's request for a flat in London so he could stay overnight on union business.