Mario Conti said the Catholic Church will actively fight against the previously “unthinkable” issue which was being considered in a “largely post-Christian society”.
He also claimed the Scottish Government does not have a mandate to “reconstruct society on ideological grounds”.
The Government is holding a consultation on whether same-sex marriage should be introduced. A similar debate is taking place south of the border.
The archbishop made the comments yesterday in a statement being sent to Scotland’s 500 Catholic parishes to encourage parishioners to complete a declaration in defence of marriage.
He wrote that while the redefining of civil partnerships as marriage may be seen as a minor step taken out of consideration for gay couples “such a determination by the Government is of serious import and will be rightly resisted by many.”
He added: “The Catholic Church, for one, will not accept it, and indeed will actively campaign against it.”
He added: “Those in Government need to be respectfully reminded that a mandate to govern does not include a mandate to reconstruct society on ideological grounds, nor to undermine the very institution which, from the beginning, has been universally acknowledged as of the natural order and the bedrock of society, namely marriage and the family.
“In terms of law, its support and defence has been on a par with the defence of life itself. We weaken it at our peril.”
The archbishop’s comments echo those of the Bishop of Paisley, Philip Tartaglia, who last week argued that a same-sex union was not marriage.
Bishop Tartaglia said: “Marriage is uniquely the union of a man and a woman, which, by its very nature, is designed for the mutual good of the spouses and to give the children who may be born of that union a father and a mother.
“A same-sex union cannot do that. A same-sex union should not therefore be called marriage.”
However, the Provost of St Mary’s Cathedral in Glasgow, the Very Rev Kelvin Holdsworth, branded the men’s comments embarrassing.
In his sermon yesterday, the Scottish Episcopal Church clergyman said: “The behaviour of our brothers, the Roman Catholic bishops, in recent days has been so unpleasant and so ill-judged that it risks harming the good influence of the whole Christian community.
“To behave as though bishops carry some kind of block vote to Holyrood, to threaten politicians and to decry those who want access to the dignity of marriage as unnatural … to say these things seems to me to go too far.”
“Such comments from the leaders of the Roman Catholic Church have left me feeling embarrassed as a Christian.”
Archbishop Conti’s comments come at the time of a serious downturn in relations between the Government and the Catholic Church over the issues of same-sex marriage and the controversial Offensive Behaviour at Football and Threatening Communications Bill.
The church has criticised the new law proposals and called them problematic.
First Minister Alex Salmond is now expected to agree to a formal review of the new bill, which is aimed at tackling disorder at football, in order to appease his critics.
It is believed he will back a call from MSPs to monitor its impact after it gets through a parliamentary vote.