The Church received complaints about Rev Richard Cameron's social media use on Wednesday.
He tweeted in September that "homosexual behaviour is a sin" and "allowing children to change their gender is wicked".
He also tweeted: "Christ has the power to help and change anyone. Obviously many gays hate this because want to carry on in their perversion."
On top of that, the minister shared a series of controversial views on Islam, describing terrorism as "a problem Islam needs to deal with", a full face veil as "oppressive and unBritish" and the prophet Muhammad as "a violent man".
The Labour Party pointed out the tweets after Rev Cameron branded Jeremy Corbyn a "terrorist sympathiser" as he was entering the Heart of Scotstoun community centre in Glasgow on Wednesday.
The Church of Scotland rebuked the minster for his statements and said it would be reviewing complaints about the his comments.
In an update on Friday, a Church spokesperson said Rev Cameron has been suspended.
"In accordance with our procedures Rev Richard Cameron has been administratively suspended," the spokesperson said.
"This is to allow us to carry out an enquiry in relation to the incident which took place earlier this week and the subsequent complaints about his social media use."
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