Prime Minister Malcolm Turnbull says a Victorian church which cancelled a couple's wedding because they expressed support for same-sex marriage was acting well within its rights.

Fairfax Media on Friday revealed a 26-year-old bride and 25-year-old man in Ballarat had their wedding plans torn up by their local Presbyterian church because the bride posted a Facebook status defending gay marriage.

In promoting the postal survey on same-sex marriage, Mr Turnbull has encouraged all Australians to have their say freely and respectfully.

But he also defended the right of the Ebenezer St John's church in Ballarat to refuse to marry the couple because of their views.

"Churches are free to marry whoever they like, you know," Mr Turnbull said.

Pressed on whether the couple had paid a penalty simply for doing what he as Prime Minister had encouraged them to do, he said: "Churches are entitled to marry or not marry whom they please. That is part of religious freedom.

"There are many churches, including my own church the Catholic Church, who will not marry someone who has been married before."

Mr Turnbull also underlined his belief in religious freedom, declaring: "As strongly as I believe in the right of same-sex couples to marry, even more strongly do I believe in religious freedom."

He promised that in the event of a "yes" vote in the survey, any same-sex marriage bill facilitated by his government would contain very strong protections for churches and religious groups.

But the PM said it was not necessary to draw up those proposed protections before the vote, because the survey question was a "threshold question of principle".

He also made the point: "The 'no' case would vote 'no' against any legalisation of SSM regardless of protections there are for religious freedom."

The Ballarat bride and groom were to be married in November at their Presbyterian church by minister Steven North.

In early August, when the Turnbull government announced the postal survey on same-sex marriage, the bride posted a Facebook status declaring her support for change.

Days later, the couple were summoned to Mr North's office and were told he would no longer marry them, nor would they be allowed to hold their ceremony at the church.

In a letter to the bride, provided to Fairfax Media, Mr North said the views expressed in the Facebook post had "practical consequences" for the wedding.

"After the pre-marital counselling that you attended and the sermons delivered at Ebenezer on this subject, you must surely appreciate that your commitment to same-sex marriage opposes the teaching of Christ Jesus and the scriptural position practiced by the Presbyterian Church of Australia and by me," he wrote.

"This conflict of views has practical consequences in relation to your upcoming wedding.

"By continuing to officiate it would appear either that I support your views on same-sex marriage or that I am uncaring about this matter. As you know, neither statement is correct.

"Also, if the wedding proceeded in the Ebenezer St John's church buildings, the same inferences could be drawn about the Presbyterian denomination. Such inferences would be wrong."

Fairfax Media has spoken to the couple but has agreed not to name them, in line with their wishes. The couple did not seek media attention about the case – Fairfax Media was informed by a friend of the family.

Ebenezer St John's did not return multiple calls. John Wilson, clerk of assembly at the Presbyterian Church of Victoria, said decisions about officiating marriages were at the discretion of individual ministers. He did not wish to comment further.