While campaigning in Glasgow on Wednesday, the Labour leader was interrupted as he explained the scarf he was wearing had been given to him by the Who Cares Scotland charity.
Richard Cameron, a minister at Scotstoun Parish Church, shouted at Mr Corbyn: "I thought you'd be wearing your Islamic jihad scarf.
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After footage of the encounter attracted attention, Labour pointed to a series of controversial tweets it said were posted by Mr Cameron, including remarks saying "homosexual behaviour is a sin" and "allowing children to change their gender is wicked".
The Church of Scotland said Mr Cameron will not be allowed to work as a minister while an inquiry takes place.
A spokesman said: "In accordance with our procedures, Rev Richard Cameron has been administratively suspended.
"This is to allow us to carry out an inquiry in relation to the incident which took place earlier this week and the subsequent complaints about his social media use."
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The account also 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".
PA has checked the account and verified that it belongs to Mr Cameron.
During his encounter with the Labour leader, Mr Cameron also said: "Do you think that the man who is going to be prime minister of this country should be a terrorist sympathiser, Mr Corbyn?'"
The Labour leader did not react and was ushered into the nearby community centre he was due to visit.
Mr Cameron then accused Mr Corbyn of "running away".
At the time, the Church of Scotland rebuked Mr Cameron for the way he approached the situation, saying: "Whilst we may occasionally robustly challenge policy issues with which we disagree, we always intend to do that in a way that is polite and measured and allows for reasoned debate."