Reverend Gary Caldwell appeared at Flowerhill Parish Church in Airdrie, North Lanarkshire, with another minister who broke the news.
Mr Caldwell is to continue his duties under the supervision of a mentor while the inquiry is carried out by a member of Hamilton Presbytery and two members of neighbouring presbyteries.
Reverend Keith Ross told the congregation on Sunday Mr Caldwell is part of a probe that also involves session clerk Malcolm Ross and retired minister Rev Jim Munton.
Several people called for a probe into claims of bullying that involved parishioners such as Dmitri Ross, a church member who is openly gay, in a civil partnership, and who tried to train as a minister but later withdrew.
The Herald understands the bullying allegations relate to a range of issues and a number of parishioners. It is also understood complaints relating to Dmitri Ross's sexuality are not included in the case at this stage.
There have been two previous investigations into the church at Presbytery level, but an appeal against the last finding was upheld and the new probe is to be launched.
Church papers reveal a Kirk Commission of Assembly, one of the Kirk's highest courts, agreed to: "Instruct the Presbytery to reinvestigate the complaint to determine if there is a prima facie case to proceed to further investigation in respect of allegations of dishonesty or bullying."
The Commission of Assembly also agreed to: "Instruct the Presbytery of Hamilton to provide mentoring for the minister of Flowerhill, appoint assessor elders to the Kirk Session of Flowerhill for a period to be determined by the Presbytery, ensure additional pastoral support is available to all parties to the original complaints and to current and former members of Flowerhill church, where possible."
A Kirk source said there was no evidence to support claims made at the court hearing that he had bullied elderly people.
One church member said allegations were made in the court hearing that the minister had bullied elderly people, but a source at Kirk headquarters in Edinburgh said there was no evidence from the appellants when they made these allegations.
A Presbytery spokesman said: "The investigation is sub judice so we shall not release any further information or make any comment until it is complete."
Mr Caldwell and Mr Munton declined to comment. Mr Ross did not respond.