Gay rights campaigner and Liberal MP Warren Entsch says an apology from the head of the Australian Christian Lobby would not make up for his "highly offensive" comments on homosexuality.

Jim Wallace has come under intense criticism after comparing the health impacts of smoking cigarettes to the health of homosexuals.

Prime Minister Julia Gillard condemned the retired SAS commander's comments and cancelled her plans to speak at the Christian Lobby's national conference next month.

Mr Entsch has told PM that Mr Wallace's statement was "stupid, spiteful and disgusting" and that an apology would not be enough.

"When I read this I thought that Jim Wallace must have been hibernating under a rock or in a cave somewhere in the deep, dark depths of the wilderness of Tasmania, maybe on the western coast somewhere, and is suddenly awakened from an absolute sleep from probably 1,000 years ago," he said.

"He's probably still walking on his knuckles. I find it highly offensive."

He says Mr Wallace's suggestion that sexuality is a lifestyle choice is "unbelievable" and congratulated Ms Gillard for pulling out of the Christian Lobby conference.

But Beyond Blue chairman Jeff Kennett says the Prime Minister should have shown up.

"If she's rejected the invitation and they wish to invite me, I'll take it up," he said.

"There's no point running away from intolerance, discrimination and racial vilification.

"If I'd been the prime minister, I would have actually gone to that conference and I would have argued the case for the sorts of things Beyond Blue are doing and I believe most fair Australians would expect."

'Demonisation tactics'

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Mr Wallace's comments were made during a debate on marriage equality with Greens leader Christine Milne on Wednesday.

He compared health statistics for smokers with those of homosexuals, pointing to figures showing that smokers were likely to live up to 10 years longer.

He is standing by his comments but argues he is being misrepresented.

"The Prime Minister's decision is made on the basis of media reporting which said that I said smoking was healthier than gay marriage," he said.

"I never said that. And my comments were much more nuanced.

"Just making the point that if we are to package gay marriage in with… or gay lifestyle in with the heterosexual lifestyle in marriage, then we are ignoring the fact that it's not equal love when the consequences of gay love... in health consequences are quite pronounced and disastrous."

He says he cannot see why his comments would be offensive to homosexuals or the Prime Minister.

"This is a victory for the demonisation tactics of gay activism and it's a constant misrepresentation and spin of anything by people who support marriage as between a man and a woman," he said.

The Greens have lodged an official complaint with the Human Rights Commission over his statements.

Earlier on Thursday, Ms Gillard labelled Mr Wallace's comments as heartless.

"To compare the health effects of smoking cigarettes with the many struggles gay and lesbian Australians endure in contemporary society is heartless and wrong," she said.

And former prime minister Kevin Rudd backed her.

"I haven't seen the text of what Mr Wallace has said, but if reported accurately they strike me as homophobic," he said.

Mr Wallace was an Army brigadier and a former special forces commander before taking on his role at the Australian Christian Lobby.

He is no stranger to controversy. On Anzac Day last year he tweeted that the Australia which servicemen and women fought for was not gay marriage nor Islamic.