The Church of Scotland's annual General Assembly yesterday voted to move towards the ordination of ministers in civil partnerships.

Last year's Assembly concluded that the Church could not condone same-sex marriages or civil partnerships, however commissioners voted in favour of a proposal that would allow individual congregations to 'opt out' of the Church's official policy on homosexuality, and could choose to employ a gay minister should a vacancy arise.

This decision has caused significant division among Christians across Scotland, and many congregations have opted to leave the Church of Scotland; choosing instead to join the Free Church, which has a firm stance against homosexual clergy.

David Robertson, minister of a free church in Dundee and director of the Solas Centre for Public Christianity, said confusion surrounding the official Church line on homosexuality has made a "laughing stock" of the Church in Scotland.

"Last year the General Assembly reaffirmed biblical teaching that same-sex civil partnerships are wrong, but then allowed ministers who are gay in. It confused people, and made a laughing stock of the Church here. They meant well, and I'm sure thought it was a brilliant compromise, but it can't work – you can't say it's wrong but we'll let you do it anyway," he told Christian Today.

Rev Jeremy Middleton, of Davidson's Mains Parish Church in Edinburgh, an evangelical in the Church of Scotland, yesterday urged the Assembly to support the notion that "marriage between one man and one woman is the only right and proper context for sexual relations".

Under his proposal, clergy in same-sex partnerships would be banned from serving the Kirk, though celibate gay ministers would not.

His proposal was rejected, however. The Assembly instead voted overwhelmingly in favour of a proposal that may lead to the ordination of actively gay ministers, with a majority of 369 to 189.  Draft legislation will now be passed to individual Presbyteries who will debate the decision, before a final vote is taken at the General Assembly in 2015.

Forward Together, a group of evangelicals within the Church of Scotland, has expressed its disappointment at the outcome of yesterday's meeting.

In a statement, the group labels the Kirk's traditional position on sexuality and decision to allow the ordination of those in civil partnerships a "blatant contradiction".

"The Assembly has once again chosen to put the so-called 'peace and unity' of the Church, which is clearly lacking, before its duty to be a Church that honours the Word of God, which is contained in the Scriptures of the Old and New Testament, as its supreme rule of faith and life," the statement reads.

"This decision will cause great pain for members of the Church who struggle with same-sex attraction but who strive to maintain a celibate life, in accordance with the clear teaching of Scripture. It will cause great distress in many congregations throughout the Church of Scotland and it will destroy relations between the Church and many of our partners in the World Church."

However, Forward Together has also urged members of the Church of Scotland who oppose the motion not to "act hastily" and leave the Kirk, but instead "to engage fully in the debate that will now take place at Presbytery level under the terms of the Barrier Act".

Under this Act, the proposal could still be blocked if the majority of Presbyteries are not in favour of the new legislation.

At the close of yesterday's debate, Right Rev John Chalmers, Moderstor of the General Assembly, praised the gracious way in which commissioners with opposing views had addressed each other, noting that, "This has been a difficult day and a difficult discussion for us all".

"From me to you, my grateful thanks it has been conducted as a respectful dialogue and a model of how these conversations should be held within the Church," he finished.

The Assembly will close on Friday May 23.