Rev Ian Powell, who serves at St Matthew's Wanniassa in the capital Canberra, approached Labor leader Bill Shorten (above) after a church service marking the beginning of parliament.
Australian politicians are currently deciding whether to give the people a referendum on whether to introduce same-sex marriage.
After the Orlando LGBT nightclub shooting, Bill Shorten reportedly said that a potential Australian referendum on gay and lesbian marriages could "give haters the chance to come out from under the rock".
According to ABC, Revd Powell told the Opposition leader: "You described people who weren't in favour of changing the definition of marriage as 'haters who come out from under rocks'.
"Can I ask you not to speak like that? Because I know lots of people like that.
"Please don't speak like that about other Australians, so we can have a civil and tolerant discussion rather than the hate that's been coming."
Mr Shorten said Revd Powell was quoting him inaccurately.
He added in response: "Please don't hector me. Give me the chance to speak.
"First of all, people of faith can be opposed to marriage equality.
"People of faith can be opposed to marriage equality but some people who object to marriage equality do have homophobic attitudes."
