Legalising same-sex marriage would "legitimise and encourage" the existence of fatherless or motherless children, according to a report.
A Free Church of Scotland study panel examined the issues surrounding marriage, divorce and remarriage.
The study comes as responses to the Scottish Government's consultation on gay marriage are evaluated.
Referring to same-sex couples, the Free Church report said: "By getting the right to marry, they get more respectability for bringing up children (they already have the right to foster and adopt).
"This is a huge social experiment in which the guinea pigs are children. That is not fair or just to children and does not safeguard their rights.
"It is really being pushed in a doctrinaire way by the gay lobby without any consideration of the harm that it will do."
The church said that civil partnerships already give same-sex couples the same legal rights as marriage, and therefore there is no need to introduce same-sex marriage.
The Scottish Government launched its public consultation stating it "tends towards the view" that same-sex marriage should be introduced but that faith groups and their celebrants should not be obliged to solemnise the ceremonies.
The Scotland for Marriage group, which is supported by some religious groups, has campaigned against the proposal while the Faith in Marriage campaign - a coalition including, among others, the United Reformed Church, the Quakers, Buddhists and the Pagan Federation - has spoken out in support.
Same-sex marriage is also supported by organisations such as the Equality Network, NUS Scotland, LGBT Youth Scotland and the Scottish Youth Parliament.
This year's Free Church general assembly is also expected to approve a recommendation that Free Church of Scotland ministers will only solemnise marriages between a man and a woman.
The church said the measure is designed to protect Free Church ministers in the event that the Scottish Government's proposals become law.
A Scottish Government spokesman said: "We have made clear that although we have expressed our initial view on same-sex marriage in Scotland, no decisions have been taken and all views will be listened to.
"An analysis of the consultation is currently under way and is likely to be published in June."