Reverend David Robertson, who is also director of the Solas Centre for Public Christianity, criticised President Vladimir Putin as "a fascist communist whose autocratic reign is the very antithesis of everything Jesus Christ is about".
Although he said he was opposed to legalising same-sex marriage, Rev Robertson condemned the hostile treatment handed out by the regime to anyone believed to be gay, lesbian, bisexual or transgender. He said: "We live in a society where even the mildest questioning of same-sex marriage is met by cries of 'homophobia' and greeted with abuse and hate mail.
"So when those same cries are made about Putin, there might be some of those who feel that because he is being accused of the same thing, we are on the same side. We are not.
"What is happening to many homosexuals in Russia is something that no Christian should have any sympathy with whatsoever.
"People are being tortured, abused and murdered with the connivance of the State."
He added: "There are no circumstances where any Christian could condone hatred, torture and abuse of any person, whether they are homosexual or not."
Scotland's local authorities have come under pressure to sever their ties with Russian twin cities after Russia's lower house of parliament passed a law allowing heavy fines to be imposed on people providing information about homosexuality to under-18s.
It has been blamed for a surge in attacks on the gay community.