A delegation from the church, which has already made clear its opposition to the idea, met a Scottish Government official earlier this week to discuss the controversial issue.
The Government has proposed either legislation or guidance to protect the beliefs of public sector workers and religious celebrants opposed to same-sex marriage.
Dr Malcolm Maclean, editor of the Free Church's monthly magazine The Monthly Record and minister in Inverness, said: "We are saddened by the determination of the Government to move away from the Christian understanding of marriage which has been the bedrock of our society for centuries.
"Further, having met with the Government official, we also remain unconvinced about the proposed protections or safeguards for ministers, teachers and other public sector workers who object to this new meaning."
During the meeting it was also revealed that words such as 'husband' and 'wife' could be set to disappear from official paperwork under the proposed new legislation for same-sex marriage, Dr Maclean said.
He added that if ministers proceed with the redefinition of marriage, there was nothing to stop the institution being further redefined in the future.
A Scottish Government spokeswoman said: "We are totally committed to protecting religious freedom and freedom of expression, and ensuring that religious celebrants opposed to same-sex marriage do not have to solemnise same sex ceremonies.
"We intend to proceed with plans to allow same-sex marriage and religious ceremonies for civil partnerships because we believe it is the right thing to do."