A church has been tagged with vile 'bash bigots' graffiti - even though it isn't telling parishioners how to vote on gay marriage.

Drew Mellor, the head pastor of Glen Waverley Anglican Church in Melbourne's south-east, discovered the spray can attack early on Sunday morning.

He was particularly upset with a tags which had threats of violence via the phrases, 'Vote Yes, bash bigots'.

The Waverley Baptist Church, at nearby Wheelers Hill, was tagged with 'Crucify No voters' at the weekend.

The Glen Waverley Anglican Church in Melbourne was sprayed with a threat of violence

The Waverley Baptist Church at Wheelers Hill was also vandalised with 'Crucify No Voters'

'That's very unsettling for some of our older members of our church this morning,' Dr Mellor told Daily Mail Australia on Sunday.

'Some asked, 'Does that mean we're going to be bashed?'.

Dr Mellor also took exception to a cross and a Nazi swastika being sprayed on either side of an equals sign.

'To see Christians in that light, that somehow we hold a view that if people don't agree with us then we're going to do something to diminish them, that's not what people of the Gospel think,' he said.

'It conveys a message that as a Christian church we are intolerant.'

Dr Mellor said he was 'saddened' to have found the graffiti at 6.30 on Sunday morning, adding he repudiated any suggestion Christians are 'bigots' who sought to harm those with different views.

Glen Waverley Anglican Church head pastor Drew Mellor (right) was 'saddened' to find graffiti

The Glen Waverley church isn't telling people how to vote on gay marriage, with Dr Mellor releasing a statement in September, which said recognising gay relationships was 'the respectful thing to do' for those inclined to vote 'Yes' to redefining marriage.

While Dr Mellor is opposed to gay marriage for Biblical reasons, he said his parish welcomed gay members.

'We certainly have ministry with, long connections with people that would align themselves with personally with the gay community,' he said.

'We wouldn't conduct a marriage service for a gay couple ... nor would we exclude anyone if they happen to be a gay couple in a marriage relationship.'

David O'Brien, the senior pastor at Waverley Baptist Church, said the 'Crucify No voters' graffiti was 'disturbing and concerning' as his congregation is urged to vote on gay marriage according to their conscience.

'It was a shock. I really couldn't take it seriously,' he told Daily Mail Australia.

'Some people blame religion and wish to have some measure of payback for what is perceived to have been slights in the past.

'It also shows we live in an era where tolerance is lessening, which is a sadness and a great tragedy of our age.'

Glen Waverley Anglican Church head pastor Drew Mellor respects the case for gay marriage

The Coalition for Marriage, which is leading the 'No' case against gay marriage as part of the $122 million postal vote survey, said the graffiti attack highlighted the intolerance of 'Yes' campaigners.

'One thing that this process has revealed is that, despite the rhetoric, 'Yes' campaigners do not actually believe in a tolerant society, where people are allowed to 'live and let live',' spokeswoman Monica Doumit told Daily Mail Australia.

'Rather, they will target those who disagree for abuse, for boycott, or for some other type of punishment.'

However, Dr Mellor said he would forgive the vandals adding the graffiti attack was not a reflection on all 'Yes' voters.

'I don't believe that's where the majority of those who are advocating equality in marriage would be coming from,' he said.

This graffiti attack comes two weeks after a Mormon church, west of Sydney, was defaced with 'Vote Yes' graffiti even though it hadn't even told its parishioners how to vote in the gay marriage postal survey.

The Church of Jesus Christ of Latter-day Saints at Leura, in the Blue Mountains, was sprayed with red and black tags.