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But Turnbull also warned cruel comments were often part of democratic discussion and could not be curtailed without impinging on free speech.
“I deplore disrespectful, abusive language whether it is directed at young gay people or people of other religions or other races,” Turnbull told Sydney commercial radio station 2DAY FM.
“So mutual respect and a respectful debate is what we should have in Australia.”
His comments come after Australia this month finalised plans for a non-binding postal vote on same-sex marriage, which is expected to be completed by mid-November.
In early signs the debate could turn toxic, a poster emblazoned “stop the fags” was put up in central Melbourne and flyers describing homosexuality as “a curse of death” were distributed in suburban Sydney.
Turnbull said extremists should not be allowed to derail the debate, urging both sides to “focus on the substance of the debate”.
“The key here is respect,” he said. “I know many people who take a conservative view of marriage… who do not have a homophobic bone in their body.
“One of the problems in debates like this is the tendency to caricature each side.”
Turnbull supports gay marriage but has been pressured to hold the nationwide postal vote, rather than simply enact reform in parliament, to placate right-wingers in his conservative government.
Critics warn the vote opens the way for a divisive debate that will subject gay people and their families to hate speech, but Turnbull said it was just part of the democratic process.
“People will often say, in any democratic debate, things that are hurtful and unfair and sometimes cruel, but that is part of a debate,” he said.
“The only way to stop people saying things that you find hurtful is to shut down free speech.”
Turnbull also dismissed concerns that the vote would be meaningless because it is non-binding on the nation’s parliament.
“If the postal vote is carried, the legalisation of same-sex marriage will sail though the parliament, believe me,” he said.
The Australian Bureau of Statistics will begin sending out ballots on September 12 and voting will close on November 7, with the result known later that month.
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