The Church of England’s governing body has passed a motion in favour of giving civil partners of deceased gay clergy the same pension entitlements as heterosexual widows or widowers.

The motion was put forward by the Rev Mark Bratton, priest at St John the Baptist church in Berkwell, near Coventry. It asks the Church of England Pensions Board to go beyond the requirements of the Civil Partnership Act 2004 and pay pension benefits to surviving civil partners of deceased clergy on the same basis as surviving spouses.

Under the terms of the Act, surviving civil partners are not entitled to benefits if their deceased partner ceased pensionable service before December 2005. At present, a widow or widower is entitled to a pension based on all of their deceased spouse’s pensionable service.

It means that a widow who had been married to her husband for only a few years would receive a considerably higher pension share than clergy who had been partnered for many years prior to the death of their partner.

Rev Bratton argued that the present pension entitlements were “unjust” and “discriminatory”.

“On what basis does the Church believe it just to treat a civil partner of long-standing as inferior in pension provision to a spouse who may have been married to a scheme member for only a very short time?” he said.

“It is rationally indefensible to refuse a change to the clergy pension scheme to benefit a civil partner of long-standing solely on the grounds of status.”

His motion was supported by the Bishop of Lincoln, the Rt Rev John Saxbee, who said the Church should “honour people with a justifiable claim now”.

“It is not a question of whether we can afford to do it, but whether we can afford not to do it,” he said. “The reputational damage done that can be done in missional terms is something that we cannot afford.”

The vote effectively gives civil partnerships the same status as marriage in the eyes of the Church and is likely to anger conservatives, who believe the Church has a responsibility to uphold the ban on same-sex unions and ordination of partnered homosexuals outlined in the 1998 Lambeth resolution on human sexuality.

One Synod member, who asked to remain anonymous, said conservative Synod members had deliberately withheld from taking to the floor to speak against the motion for fear of reprisals.

“They didn’t dare to. There would have been screams of homophobia if anyone had dared oppose it,” he said.

Synod members also voted down a less controversial amendment to the motion that would have broadened equal pension rights to include any relatives of clergy who had lived in their households for five years, as well as an amendment seeking to replace equal pension rights with hardship grants.

In the Twitter and blogosphere, liberal and conservative Christians alike have interpreted the vote as a signal that the Church of England has gone “pro-gay”.

Peter Ould, blogger and Anglican priest in the Diocese of St Albans, tweeted that conservative Synod members had “failed to realise it was a gay marriage debate by proxy”.

He tweeted: “If things are equal then it is unjust to treat separately. If things are not equal it is not unjust to treat separately.”

There were some concerns that the decision to afford gay clergy the same pension rights would put additional pressure on the existing deficit in the Church’s clergy pension scheme, which stood at more than £350 million at the end of 2008. The average pension for each surviving partner or spouse is expected to cost the Church £58,000.