The ban was imposed in 2009 when controversy broke out over the appointment of Scott Rennie as the Church’s first partnered homosexual minister.

After a six-and-a-half hour debate, the General Assembly voted by 351 to 294 to set up a theological commission charged with preparing a report on same sex civil unions and the implications of lifting the ban on gay ministers. The report will be debated at the 2013 assembly.

The vote has horrified traditionalists in the Church, who warn of a possible split.

Addressing the General Assembly in opposition to the proposal, the Rev Andrew Coghill, of the Isle of Lewis, likened the impact of the ordination of homosexual clergy to that of a “hand grenade”.

“We’re being asked to pull the pin out and it will blow the Church apart,” he said.

The Moderator of the General Assembly, the Rev David Arnott followed the debate with a call for unity.

“We very much hope that people who disagree with what has been decided will remain within the Church and work with us as we seek to find a way forward,” he said.

“I have had many expressions from commissioners today that they are willing to work for the greater good of the Church.”

A report presented to the General Assembly yesterday pointed to a Church deeply divided over homosexuality.

In a survey of 22,000 Church of Scotland members, nearly 60% said a person in a same-sex relationship should not be permitted as an ordained minister in the Church.

Around one fifth of those surveyed said they would “consider it obligatory” to leave the Church of Scotland if the General Assembly were to allow people in committed same-sex relationships to be ordained as ministers.