Annabelle Fuller complained of being "hounded" after an MEP challenged Farage on the rumours in the European Parliament.
Nikki Sinclaire, who left the party after a row with Mr Farage, said during a plenary session this morning: "With unemployment still a problem across Europe and indeed across the UK, does Mr Farage think it is a fair use of taxpayers' money, namely his secretarial allowance, not only to employ his wife Kirsten but his former mistress Annabelle Fuller?
"Is this a responsible use of taxpayers' money, Mr Farage?" Farage responded: "I don't want to answer that at all, thank you."
In a statement this afternoon, Fuller said: "I have been continually hounded by the press with these false allegations since 2006 including having journalists camp outside my house.
"It's a shame that as a woman I am considered fair game for accusations of alleged affairs. It's hard enough being a woman in politics without having to justify why I am employed.
"It is safe to say that this would not have happened if I was a man. Surely this is something that Nikki Sinclaire should have considered."
Fuller worked for Ukip for many years before leaving for a stint as a public relations consultant, and has now returned as a spin doctor for the party.
Farage is understood to have denied allegations of an affair with Miss Fuller in the past.