Federal Opposition Leader Bill Shorten has been accused of intolerance and "brutal" language towards people opposed to same-sex marriage, in a confrontation with a rector outside a church service this morning.

Key points: Bill Shorten confronted by Canberra Anglican church Rector

Bill Shorten confronted by Canberra Anglican church Rector The Rector took issue with Mr Shorten calling those opposing same-sex marriage 'haters'

The Rector took issue with Mr Shorten calling those opposing same-sex marriage 'haters' Rector Powell has previously linked same-sex marriage to polygamy

Mr Shorten was among politicians attending the service to mark the start of the parliamentary year.

The Labor leader is a vocal advocate of same-sex marriage, but has raised concerns a plebiscite would be divisive and encourage the vilification of same-sex couples.

Rector Ian Powell, from a Canberra Anglican church, took the opportunity to raise concerns about Labor's approach.

"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?" Rector Powell said.

Mr Shorten said he was not being quoted accurately and did not want to be hectored.

"People of faith can be opposed to marriage equality, but some people who object to marriage equality do have homophobic attitudes," he said.

After the altercation, Rector Powell called on Mr Shorten to lead the debate rather than bring it down.

"We'd like our leaders not to speak the speak that makes it vicious and intolerant, people differ on this and I know it's a passionate issue," he said.

"It was a brutally unfair way to summarise people who differ with him. If we're going to have a sensible, intelligent, tolerant discussion, our leaders need to model that rather than taking cheap, nasty, untruthful shots at people."

The rector was referring to comments Mr Shorten made in a debate during the election campaign.

During the exchange with the Prime Minister in June, Mr Shorten made reference to the Orlando shootings and raised concerns about how the debate over same-sex marriage could be inflamed in Australia.

"I don't believe that people's relationships and love for each other need to be submitted to a public opinion poll. And I think we've seen two terrible events in the last week which show that hate and extremism does exist in modern societies," he said.

"I don't want to give the haters a chance to come out from underneath the rock and make life harder for LGBTI people."

Rector Powell, who came to Canberra late last year, has previously spoken on the "unhelpful heat and anger and simplistic sloganeering" in the same-sex marriage debate.

In a 2015 address, he said debates around same-sex marriage got "very ugly, very often".

"Almost everyone on both sides is trying to help humans flourish — we just strongly disagree on it."

He also used the address to link same-sex marriage and polygamy.

"Frankly, it [plural marriage] cannot be resisted and when people say it's not even going to come to the table they're just, they're either ignorant or fibbing because we know from all around the world it is," he said.

He also cited an episode of the ABC's Q&A program, in which he said one panellist had a "snarling" attitude towards NSW politician and Reverend Fred Nile.