John Atkinson's complaint against Mr Gill is being dealt with by the Employment Tribunals Service in Cardiff.
A decision is expected in the next few weeks on whether it is thrown out or goes to a full hearing.
Mr Gill disputes the claim, saying he had adhered to the law "fully".
The leader is now both a MEP for Wales and a North Wales AM.
Mr Atkinson was Mr Gill's constituency manager in his role as an MEP, and was also UKIP's campaign manager in Wales for the 2015 general election and the 2014 European election.
He has claimed he was dismissed by Mr Gill after complaining about being asked to carry out campaigning for UKIP instead of organising his MEP constituency work, which he said went against the conditions of his contract.
It is understood he wanted to carry out office-based work as he was unable to walk long distances because of asthma.
Mr Atkinson was dismissed as Mr Gill's constituency manager in March 2016. He had been in the job since July 2014.
He resigned from the party in February because he disagreed with UKIP's internal rows over the selection of candidates for the assembly election.
A tribunal judge will now consider the next step, and a spokesman for the Employment Tribunals Service confirmed that the case is progressing.
Mr Gill said he followed the rules of the conciliation service ACAS and the European Parliament's own legislation when the contract was terminated.
He said: "I ensured that the process of concluding the contract of employment was transparent and fair in terms of paid holiday, final remuneration and notice period, and fully adherent to the law.
"I have every reason to believe that there are absolutely no grounds for any claim of unfair dismissal."
The former constituency manager for UKIP Wales leader and MEP Nathan Gill has claimed he was unfairly sacked on disability grounds.