Bishop Joseph Toal, who is in temporary charge of the Motherwell Diocese, will also appeal to supporters of Father Matthew Despard to help bring him into line.
Last year Despard, the parish priest at St John Ogilvie's Church in High Blantyre, Lanarkshire, self-published a book, Priesthood In Crisis, which alleged that the Catholic Church in Scotland was dominated by a "powerful gay mafia".
He also claimed sexual misconduct had been rife for decades within seminaries where young priests are trained.
In November, Despard was suspended from practising as a priest, with the news broken to parishioners just before mass.
The Sunday Herald revealed how angry scenes broke out among the congregation - described as "close to a riot" by one witness - when Toal informed them that "a penal judicial process" had been instituted against Despard as a result of his book.
In a letter to be read out to every parish in Motherwell Diocese today - and at masses held last night - Toal said he felt it was necessary to continue the canonical case instigated by the former Bishop of Motherwell, Joseph Devine, before he stepped down from his role.
He said: "When I met with the diocesan priests after becoming apostolic administrator in May last year I was made aware of how troubled and distressed they felt by the publication of Father Matthew Despard's book.
"Through the succeeding months I have often heard of further concern and anxiety for those named or referred to in this book, both clergy and laity. It has been necessary for me to support those whose integrity has been questioned in this publication, and to continue the canonical process initiated by Bishop Devine through which Father Despard's actions in publishing this book will be judged."
He said that being aware of the "distress" within the diocese, he took the decision that Despard should stand down from his duties, live outside his parish and not be permitted to carry out any public ministry while the process is ongoing.
But he claims Despard is refusing to accept the disciplinary process.
He added: "Father Despard finds it difficult to accept this and indeed questions my authority to take any action in his regard. I have tried to carry out the responsibilities given to me, and continue to ask Father Despard to do what I have requested.
"I would ask those who continue to support him to prevail upon him to obey my instructions."
Priesthood In Crisis was published on Amazon but has since been withdrawn. It was published following the scandal over disgraced Cardinal Keith O'Brien, who resigned as head of the Catholic Church in Scotland last February after three priests and a former priest made allegations of inappropriate sexual behaviour by him.
O'Brien was reportedly exiled from Scotland by the Vatican after apologising for his actions.
In his letter, Toal said he acknowledged the "distress and pain" caused by revelations of sexual misconduct and abusive behaviour by "some Scottish clergy", particularly in the last year. He also warned that "further allegations" of sexual misconduct "may well arise".
He added: "It is wrong to assume or to imply that all priests are suspect because of the failings of a few and it is necessary to uphold and defend the good name of our priests.
"Please be careful in jumping to conclusions and accepting at face value all that is printed or made public in the media.
"Freedom of speech is a necessary part of living in society but it has to be supported by regard for the truth and the proper protection of others' good name and character."
The affair has split Despard's congregation. A petition calling on him to be reinstated was signed by 1000 people. However, his actions are believed to have alienated others.
Sadie Polockus, 61, from Blantyre, was a former treasurer in the parish but claims she was summarily asked to leave by the priest six years ago.
She said: "If the things he said happened in the book took place, then I feel sorry for him. But I sincerely hope and pray he is removed completely from the church.
"For someone to come into our parish and decimate it - that's the only word I would use - has been absolutely terrible.
Despard was not available for comment.