The issue has risen to the top of the church agenda following a recent government report recommending the introduction of a new gender-neutral marriage law.
If parliament pushes through the bill, as seems increasingly likely, the church will be forced to either lawfully wed homosexual couples or abstain completely from the legal element of the marriage ceremony.
With this prospect in mind, the church's liturgical committee decided to look into the matter more closely. Having weighed up the pros and cons, the committee eventually recommended the Church of Sweden to continue performing legal weddings.
But there is strong opposition to the move within the church, with two representatives tabling motions calling for the church to consider abandoning the legal element of the wedding ceremony. Instead couples would be legally wed in a civil ceremony before later going to the church, mosque or synagogue to receive God's blessing.
Archbishop Anders Wejryd said he expects the issue to resurface if there is a change in the law.
"Those who voted did so on the basis of current legislation. If the law changes, the issue will return," he said.
But the Archbishop added that he was not unduly worried by the prevailing differences of opinion.
"I think the type of discussion we have had contributes to our cohesiveness. It has been an honest discussion that shows our great willingness to live together within the church. So it doesn't worry me.
"I am not of the opinion that everybody in the church should agree with each other. We have to be mature enough to live with a variety of opinions," said Wejryd.