In a report due to be considered by the church’s general assembly next month, officials have warned the organisation could be “vulnerable to legal challenge”.
This is due to possible discrimination under the European Convention of Human Rights.
The report by the Church’s Legal Questions Committee (LQC) says: “The scheme enables bodies, such as the Church of Scotland, and individual celebrants to be authorised to conduct different sex marriages while at the same time refraining from seeking authorisation to conduct same sex marriages.
“This legal structure may be argued to be discriminatory contrary to Articles 12 and 14 of the European Convention on Human Rights.”
There are discussions the Church could potentially pull out of solemnising all marriages, but the report argues that this would “rob ministers of one significant and evangelical opportunity” as marriages are an “important aspect of their ministry”.
Concerns were also raised that any legal challenges could cause “financial” and “reputational” damages to the Church and any individual ministers involved if a case was upheld.
Legislation for same sex marriage came into force in December, which the Scottish Government says protects those who do not wish to conduct ceremonies.
But the LQC argues that if a legal challenge to the scheme was successful it would be repealed and likely replaced with a system where those who wish to carry out different sex marriages must also oversee same sex marriages.
The report adds: “It might mean the exclusion of churches which are unwilling to instruct their clergy to conduct same sex marriages from an important part of the life of the nation.”
A recent Scottish Social Attitudes Survey showed 68 per cent of people supported same sex marriages.
The Kirk’s official policy is opposition to gay marriage and would have to change its rules to give ministers and deacons the choice to conduct ceremonies.
In its conclusion, the LQC report said: “The Church and Society Council recognises the important social and pastoral role played by ministers and deacons in relation to marriages, and welcomes the commitment of the Scottish Government in seeking to maintain that role in changed circumstances.
“The Council therefore supports the conclusion that this should continue unless and until the intended safeguards prove inadequate.”
A Scottish Government spokesman said: “The Scottish Government has established a robust legal framework so that the position of religious bodies who do not wish to take part in same sex marriage is fully respected.
“The systems for authorising celebrants for opposite sex marriage and same sex marriage are entirely separate and the legislation provides that there is no obligation to opt into same sex marriage.
“In addition, the UK and Scottish Governments worked together to amend the Equality Act 2010 to make it clear that refusing to marry a same sex couple is not a breach of equality requirements.”