Rev Bill Wallace said he believed Kirk law to be flawed as the accused, Rev Gary Caldwell, was unable to take the floor to defend himself in the Kirk court that called for an investigation.
Rev Caldwell, of Flowerhill Parish Church in Airdrie, North Lanarkshire, session clerk Malcolm Ross, and church member the retired Rev Jim Munton are being investigated after allegations were made against them in the Kirk court.
However, they were unable to answer the claims as the Commission of Assembly hearing was an appeal against a decision by Hamilton Presbytery, which had earlier found the accused had no case to answer. Therefore, it was the Presbytery representatives who addressed the court.
A review of judicial procedures is under way at the Church of Scotland and the Commission of Assembly that raised concerns will be scrutinised as part of that process.
Retired Rev Wallace, based in Banchory, Aberdeenshire, said the system was unjust. The former head of the Church's board of social responsibility said: "Ministers and elders cannot be assured of justice until the present system, which is biased in favour of complainers, is abolished. They could have suspended procedures while it was reviewed, but that would have had to a have happened at a General Assembly.
"None of the people that will be investigated were allowed to give their version of events at the Commission of Assembly.
"The reason was the appeal was against an earlier decision by Hamilton Presbytery so it was Hamilton Presbytery who had to answer it."
The review into judicial proceedings is due to be reported at the next annual gathering of Kirk leaders in May.
A Church of Scotland spokesman said: "We're not going to comment on Rev Wallace's assertions while the review of judicial proceedings is underway. "
Rev Caldwell is to be "mentored" by another minister while the investigation is under way and "assessor elders" are to oversee the parish.
Several people called for a probe into claims of bullying that involved parishioners such as Dmitri Ross, who is openly gay and in a civil partnership, who tried to train as a minister but later withdrew.
The bullying allegations are understood to relate to a range of issues and parishioners, while complaints relating to Mr Ross's sexuality are not included in the case at this stage. There have been two investigations into the church at presbytery level, but an appeal against the last finding was upheld.
Rev Caldwell received support from a neighbouring clergyman, Rev Alan McKnight of Plains Evangelical Church.
In a letter to The Herald, he said: "Far from him being a bully he has been the victim of merciless bullying for almost three years now."
He said the "terrible treatment of these godly men" had roots in the "wider political machinations of the Church of Scotland in relation to acceptance and recognition of homosexual clergy".