PRIME Minister Julia Gillard will boycott the annual conference of a major Christian group because of its "heartless" attitude towards homosexuals.

Ms Gillard was to have given the keynote address to the Australian Christian Lobby next month but today cancelled her appearance.

She accused ACL managing director Jim Wallace of offensive comments Wednesday when he compared gay marriage with the health risks of smoking. Mr Wallace repeated his comments in a statement today.

The Prime Minister has said she opposes gay marriage but today took the significant step of defending those who are agitating for law changes to allow it. In political terms the Prime Minister was ensuring she did not lose the influential gay vote in inner city areas.

"There is a range of deeply held views in the community on the issue of same-sex marriage but it is the responsibility of all parties in this debate to be respectful and responsible in any public comments they make," the Prime Minister said today in a statement.

"I believe yesterday's comments by Jim Wallace were offensive. To compare the health effects of smoking cigarettes with the many struggles gay and lesbian Australians endure in contemporary society is heartless and wrong.

"Although everyone is entitled to their own view, these statements reiterated again today on behalf of ACL are totally unacceptable. In light of this, I believe my attendance at the conference would be inappropriate."

Mr Wallace, who is also a former head of the SAS, made his comments during a debate on gay marriage with Greens Leader Christine Milne in Hobart yesterday.

"I think we're going to owe smokers a big apology when the homosexual community's own statistics for its health - which it presents when it wants more money for health - are that is has higher rates of drug-taking, of suicide, it has the life of a male reduced by up to 20 years," Mr Wallace said.

"The life of smokers is reduced by something like seven to 10 years and yet we tell all our kids at school they shouldn't smoke.

"But what I'm saying is we need to be aware that the homosexual lifestyle carries these problems and ... normalising the lifestyle by the attribution of marriage, for instance, has to be considered in what it does encouraging people into it."

In his statement today Mr Wallace attacked 'gay activists' he said had misrepresented his comments about smoking in a deliberate attempt to demonise and to shut down debate.

"I was not comparing homosexuality with smoking at all. What I was saying is that on one hand we are vocal on our discouragement of people to smoke and on the other we are suppressing public dialogue about the health risks associated with homosexuality," he said.

"Instead of more free speech-suppressing vitriol and demonisation from the gay activists, there needs to be an open and honest debate before Parliament changes the definition of marriage."

The ACL said the prime minister's decision to pull out of the conference would be seen "as the abandonment of the Christian constituency".

It said the Prime Minister’s decision was disappointing and based on inaccurate reporting “and misrepresentation by gay activists”. It had been a blow to free speech.

“This is a victory for the relentless campaign of demonization against anyone who would challenge the gay activists’ agenda in the public square,” said Mr Wallace.

“What I did say is that heterosexual sex and homosexual sex are different and have different health consequences. They should not be packaged the same way as marriage because, as just one of many reasons, they are different.

“If we warn against smoking because it carries health dangers, we should also be warning young people in particular about activity which clearly carries health risks.”

Mr Wallace also roused controversy on ANZAC Day last year when he Tweeted "Just hope that as we remember Servicemen and women today we remember the Australia they fought for wasn't gay marriage and Islamic!"

Ms Gillard was to have delivered the keynote address at the annual ACL conference in Canberra on October 5. The conference theme will be "Building a nation OF character: Religious freedom in a secular democracy."

Other speakers will include Mr Wallace; Greg Craven, Vice-Chancellor of the Australian Catholic University; Liberal front bencher Kevin Andrews; lawyer Elizabeth Turnour; and Paul Henderson of Compass Australia.

The Greens Christine Milne today said the ACL was more a company than a lobby group and was not linked to any Christian church.

“The Prime Minister should not be going anywhere near the ACL,” said Senator Milne.

Australian Marriage Equality convenor Alex Greenwich praised Ms Gillard for taking a stand against the extremism of the Christian lobby.

Mr Greenwich called on Mr Wallace to apologise for the comments, saying they were based on fear rather than facts.

- with Phillip Hudson