An anglican priest has been given permission by his church to conduct controversial civil union ceremonies.

The vicar of St Columba's Church in Grey Lynn, Hugh Kempster, will only be allowed to conduct the services in a private capacity but the compromise has upset some conservative clergy.

Kempster is applying to become a civil union celebrant which will allow him to conduct ceremonies on behalf of  gay and lesbian as well as defacto heterosexual couples from late April.

Although Kempster will soon be presiding over civil unions they won't take place within the walls of his church.

"I've spoken to my bishop about my stance and he's given me permission to be a civil union celebrant or to apply to be a celebrant but in a capacity as a private individual," he said.

But others within the anglican clergy think the two roles are incompatible.

"It's always interesting when a priest thinks they've got a private life as though being a priest stops at a certain day or a week," says anglican priest Peter Carrell.

Churches have been grappling with gay issues for years.

The anglican church has no position on civil unions and its bishops failed to reach agreement on the issue last year. The presbyterian church is also yet to decide its stance but the catholic church says its priests will not be given permission to conduct civil unions.

"If he's committed to the church's teaching he's hardly going to be blessing a relationship that's regarded as immoral," says Bishop Peter Cullinane.

Civil union licences will be issued from April 26.