The Reverend Donald Michael MacInnes made the comments on a Facebook page read by parents of children at Glasgow Gaelic School, in reference to the Scottish Government's proposed same-sex marriage legislation.
In the post the Church Of Scotland minister repeatedly refers to homosexuality as a disorder and adds: "We can now expect to see the school curriculum changed to the end that our children will be taught this perversion as if it were a good thing."
Parents at the non- denominational school, complained to education officials about the post, where he also said: "Many of us have great sympathy with those who suffer from this disorder."
The school, in Berkeley Street, near Charing Cross, provides Gaelic medium education for pre-school, primary and secondary pupils.
One parent said: "I don't want my children exposed to any sort of prejudice from a person in authority and I would not be confident of other views he might express directly to the children."
Another commented: "Absolutely disgraceful. It is not a disorder, you cannot choose your sexuality."
A spokeswoman for Glasgow City Council said that while the minister was entitled to his opinions, action had been taken because his views "were not in keeping with the ethos of the school" and the council had a duty of care to pupils.
Reverend MacInnes, who is minister of Gairbraid Church in Maryhill, is originally from Lewis, Outer Hebrides, and is the former minister at St Columba's Church in St Vincent Street.
In the post, he described the Government's decision to pursue same sex legislation as a "tragic day" for Scotland. He said: "The overwhelming support of our Scottish politicians in creating Same-Sex Marriage is very disappointing.
"Many of us, myself included, agreed that the creation of civil partnerships was necessary so that individuals suffering from this disorder were not legally penalised in any way because of their sexuality.
"We can now expect to see the school curriculum changed to the end that our children will be taught this perversion as if it were a good thing."
A council spokeswoman said: "The school did receive complaints from some parents about the inappropriate comments made and a decision was taken to review the religious observance at the school."
The minister declined to comment when approached by the Evening Times.
In September, an investigation was launched after it emerged children at an East Kilbride primary were being given religious instruction by an extremist American sect that condemns homosexual relationships and does not believe in evolution.
Volunteers from the West Mains Church Of Christ were dismissed by the council and two head teachers were removed from their posts at Kirktonholme Primary.
It later emerged the school's new chaplain, Lenny Prentice, is from a church with the same beliefs. He is an elder at the same church - Westwoodhill Evangelical - as Dr Nagy Iskander, widely described as one of Europe's top creationists.