The church's Sydney diocese, renowned for its conservative bent, drew down its massive Diocesan Endowment about one month ago to support the fight against legalising same-sex marriage.

Archbishop Glenn Davies revealed the donation at the opening of the 51st Synod on Monday, declaring same-sex marriage "unwarranted". "The stakes are high and the cost is high," he said.

Barney Zwartz, spokesman for Melbourne Archbishop Philip Freier, confirmed the diocese in the Victorian capital had not and would not make a donation to the Coalition for Marriage.

Rebel clergy in Sydney were openly fuming about the decision on Tuesday, pointing to diverse views among Anglicans on same-sex marriage, and other social issues on which the money could have been spent.

"I'm shattered," said Reverend Dave Smith, parish priest at Holy Trinity in Dulwich Hill. "I think there's a degree of shock [among the congregation]. I think they are taking it pretty hard."

St James' rector Father Andrew Sempell was so enraged by the decision he wrote a paper in response to Archbishop Davies, which he hopes to present at the ongoing Synod.

He told Fairfax Media he was "surprised" to learn of the donation, which was made by the "more secretive" Standing Committee of the diocese.

"There was no consultation, there was no open debate - and therefore no transparency in the decision," he said.

"We haven't let go of Christendom all that much. We still think that we have a right to tell people what to do. This is one of the reasons we're on the nose."

Father Sempell also cited the poor financial management of the diocese in recent years, which saw its assets crumble amid the global financial crisis.

"They did everything wrong that you could possibly do," he said. "Which sort of begs the question: why are they throwing money around like this?"

The $1 million donation was not taken from parishes but from the Diocesan Endowment, run by the Glebe Administration Board. According to the annual report of the Sydney Diocesan Secretariat, the fund grew by $13.7 million last year, or 9 per cent.

The diocese stood by the donation on Tuesday, noting it was in line with the long-standing position on same-sex marriage adopted by the Synod.

Bishop Michael Stead told Fairfax Media it was "totally appropriate" and "money well spent" given the significance of the issues at stake.

But the donation was even criticised by Anglican priests inclined to vote "no", such as Reverend Michael Paget of St Barnabas on Broadway.

In a Facebook post, he said it was "out of proportion" with the church's spending on other social issues, amounted to "poor financial stewardship" and was close to "indefensible".

Reverend Paget said the decision would "disproportionately affect churches with large numbers of young adults" - including his own, whose congregation has an average age of 25.

The $1 million boost to the Coalition for Marriage has helped keep on air a number of television advertisements warning of "consequences" of same-sex marriage, including "radical sex and gender programs" in schools.

The Equality Campaign received a $1 million donation from Qantas boss Alan Joyce, but both sides have claimed to be the financial underdog.

"We all know that the opponents of equality have radically outspent the 'yes' side," Equality Campaign executive director Tiernan Brady said on Tuesday. "They have a bottomless well of cash."

Reverend Keith Mascord, whose licence to preach in Sydney was cancelled by Archbishop Davies last year over his stance on same-sex marriage, said he was "appalled" by the donation.

"This is one of the most foolish things to have become so heavily involved in," he said. "It just seems so short-sighted and bordering on immoral because of the damage and harm it is doing."

Reverend Mascord, a founding member of the pro-LGBT Christian group Equal Voices, said the donation would be opposed by a "significant" portion of Sydney's Anglican community.

"It's blindness. It's like they're living in a bubble," he said of the church leadership. "It's counter-productive, I think that's the thing that's bothering conservative Christians."