The Scottish Government said Alex Salmond and Cardinal Keith O'Brien had an "entirely amicable" telephone conversation on Saturday on first-name terms.
It had earlier been reported that the Cardinal had "suspended communication" with the Scottish Government over its stance on the matter.
The Catholic Church in Scotland opposes same-sex marriage, which the Scottish Government last month announced plans to legalise.
Deputy First Minister Nicola Sturgeon said they would bring forward a Bill that could see the first same-sex marriages take place at the start of 2015.
The Holyrood administration insists protections will be included in the law to ensure churches, and individuals within them, do not have to conduct same-sex marriages if they do not agree with them.
The Catholic Church has described the move as a "dangerous social experiment on a massive scale".
During their phone conversation Cardinal O'Brien and the First Minister discussed several issues including same-sex marriage.
A spokesman for Mr Salmond said: "It is the right and proper way forward that officials from the Church and government are going to meet to discuss the important matters of protecting religious freedom and freedom of expression.
"It is inevitable government ministers will not always agree with church leaders – this is an honest disagreement about an important policy issue, and we have the utmost respect for the different views expressed in the debate."