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 his post, the Church of Scotland minister added: "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 Glasgow City Council spokesman said: "The man is no longer the chaplain at the school and this decision was taken as soon as we received the complaints from parents and reviewed the situation."
Parents of children at the Charing Cross non-denominational school complained to officials about the post, where he also said: "Many of us have great sympathy with those who suffer from this disorder."
The school 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 said: "It is disgraceful. It is not a disorder."
The 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.
She added: "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."
Reverend MacInnes, who is minister of Gairbraid Church in Maryhill, Glasgow, is originally from Lewis and is the former minister at St Columba's Church in the city centre.
In the post, he described the decision to pursue same sex legislation as a "tragic day".
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."
The minister declined to comment.
In September, an investigation was launched after it emerged children at an East Kilbride primary school were being given religious instruction by an extremist American sect that condemns homosexual relationships and does not believe in evolution.
Volunteers from the town's West Mains Church Of Christ were dismissed by the council and two head teachers were removed from their posts at Kirktonholme Primary.