The House of Representatives has overwhelmingly voted against legislation that would have allowed same-sex couples to marry.

Just 42 MPs supported the private members bill put forward by Labor backbencher Stephen Jones, while 98 MPs voted against.

The vote was held not long after it was announced that Liberal senator Cory Bernardi had resigned as a parliamentary secretary over comments he made linking gay marriage to sex with animals.

Labor frontbencher Anthony Albanese, who backed the legislation, says the vote shows there has been significant progress towards legalising gay marriage.

"Just a few years ago there wouldn't have been the support of anything like 42 votes on the floor of the national Parliament for a marriage equality bill," Mr Albanese told reporters soon after the vote.

"All the figures show that there is majority community support on this issue... and I think at some future time, Parliament will catch up with the community opinion."

Labor MPs had been given a conscience vote on the legislation, but Coalition MPs were expected to follow the party's position on the issue, which does not allow for any change to marriage laws.

Prime Minister Julia Gillard and her deputy Wayne Swan voted against the legislation, while many of their Cabinet colleagues voted in support of the change.

Mr Jones said even though the vote had been lost, he has claimed victory in securing public support for the change.

"Clearly we've won the debate in the Australian community - over 62 per cent of Australians believe that we should make laws to allow for marriage equality," he said.

"Unfortunately we haven't won the debate in the Australian Parliament.

"In the words of another great Australian, 'maintain your rage', because I'm quite confident that in about 10 years' time, some or all of us are going to be attending a same-sex marriage that will be both conducted and recognised here in Australia."

There are three other bills currently before Parliament that would have the same effect as Mr Jones's bill. It is unclear at this stage when they will be brought on for a vote.

'Slap in the face'

Same-sex marriage campaigners have described today's result as a "slap in the face" to gay and lesbian Australians who want to marry their partner.

The head of the group called Parents and Friends of Lesbians and Gays, Shelley Argent, says it is not fair that homosexual people are viewed as "second-rate" citizens.

"I think this Government - the whole of the Parliament that voted against this - should just be ashamed," Ms Argent told reporters.

"What I found actually really quite sad this morning was... I know that there were several of the Coalition members sitting there voting against it, where I know that they're actually very much in favour of equality."

Liberal frontbencher Malcolm Turnbull, who has spoken out in favour of same-sex marriage laws, voted against the legislation because of Mr Abbott's decision not to allow a free vote on the issue.

The head of the Australian Christian Lobby, Jim Wallace, who came under fire for comparing the health effects of smoking with homosexuality, has thanked those MPs who voted against the legislation.

"I would like to thank the Opposition for keeping its election promise and for all those members of Labor who, as a matter of conscience, voted to ensure that marriage remained between a man and a woman," Mr Wallace said in a statement.

He says most Australians were now keen to move on from the debate.