In an angry snub to the First Minister, the leader of Scotland's Catholics declined face-to-face talks on the proposed legislation in protest at his views "constantly being ignored," a Church spokesman said.
The Church warned the SNP Government must begin to address its concerns about the role of school teachers under the new laws for the cardinal to re-engage personally.
Catholic Church spokesman Peter Kearney said: "The climate is strained between the Church and the Government. We do want dialogue, but it is very hard when all the points we make are constantly being ignored.
"We really need the Government to address the substance of our concerns.
"The Government talks about protecting religious celebrants, but for us that is a complete red herring. We want to stop hearing it. Our concern is about the wider impact on society.
"For example, it will presumably become illegal for a teacher to tell a child that marriage is the relationship between a man and a woman. What will be done to protect their religious convictions or prevent them from using a same-sex storybook?"
Health Secretary Nicola Sturgeon has promised legislation to protect religious celebrants who oppose the notion of same-sex marriage.
She said schools will be unaffected as the Catholic Education Service will retain control over the content of lessons.
Church and Government officials will continue to discuss the proposed legislation with the first gay marriage likely to be held in Scotland by early 2015.
The First Minister's spokesman said the two men shared an "entirely amicable conversation on first-name terms".
He added: "While this is an honest disagreement over policy, on a personal level relations between the First Minister and the cardinal are extremely good, as they are with Scotland's other faith leaders. Mr Salmond holds the cardinal in the highest regard and will always do so."
Ministers decided to press ahead with legislation despite two-thirds of those who responded to the consultation saying they were opposed.