Misty Thackeray also said Catholicism was based on "fascist ideology" and complained of a "suffocating culture of anti-loyalism" in Scotland's largest city. He criticised attempts to curb a protest by the far-right Scottish Defence League.
SNP MEP Alyn Smith last night called on Thackeray to be removed.
Ukip, an anti-EU party, is in the throes of a civil war in Scotland. Key figures quit their posts recently while Scottish leader Lord Monckton was fired. That led to Thackeray, who works in the security industry in Glasgow, becoming acting chair.
But the Sunday Herald can reveal that Thackeray is under fire for a series of Facebook posts on religion.
He wrote in 2011: "Real Catholicism and Real Islamism are far from antagonists with both having an outwardly benign image but inwardly sharing a fascist ideology of extreme submissive conservatism and imperialism ..."
Later, he aimed a barb at Holyrood: "[T]here's more chance of winning the lottery two weeks running than getting an openly Rangers-supporting MSP into the chamber of the institutionally catholicised pretendy parliament .. lol."
He also criticised the local authority: "No wonder the blue half of my city say G.C.C actually stands for the Glasgow Celtic Council for Gays Catholics Communists eh.lol. NS!"
He wrote in 2011: "You have to witness a Glasgow election count night to understand the extent of islamist influence within the SNP and Labour … last time out I thought we were contesting a seat in Pakistan.lol."
Alyn Smith said: "These racist, bigoted and homophobic comments are totally unacceptable."
Thackeray said: "It is rather difficult to respond with any degree of accuracy to random comments allegedly made on a social network several years ago and now presented out of context by a newspaper with a clearly anti-Ukip editorial line. Such comments when taken in context would be considered merely routine social commentary by any experienced observer of Scottish political and cultural life."
He added that freedom of expression was a human right, saying he believed "very strongly in upholding these hard-won freedoms", and claimed "many in today's society have become accustomed to sugar-coated language", but stated that "it goes without saying it is never my intention to cause needless offence".