Anthony Finn, the former head of the General Teaching Council for Scotland, the profession's regulatory body, said Catholic headteachers believed the approval policy was being implemented inconsistently in different parishes.
The comments have been backed by anecdotal evidence from Catholic teachers.One said she had been asked by a priest whether she was "still living with her boyfriend" when seeking approval. Another claimed that being in a same-sex relationship had counted against him.
However, other staff spoke of being waved through without being asked about their lifestyle.
Although non-Catholics who want to work in denominational schools are also required to get approval, they are asked to give a reference, which is seen by some as an easier route to employment.
Mr Finn, honorary chair of education at Glasgow University, spoke to Catholic headteachers as part of a wider assessment of denominational schooling for the institution's annual Cardinal Winning lecture.
He said: "A number of headteachers.... had concerns about aspects of the operation of approval in practice.
"Some told me the pattern of granting approval was not always consistent, with some priests signing off forms for teachers whom they hardly knew, while others sought to apply very rigorous and perhaps unreasonably high standards."
Mr Finn also warned headteachers faced a separate "dilemma" over whether to choose the best teachers - or those from the Catholic faith.
He added: "At times of teacher shortage or, as is currently the case, when employers are reducing staffing complements, heads can face a clash of priorities.
"If you had to choose between a very good teacher who is not Catholic and what we might best describe as an adequate Catholic teacher, which would you choose?"
The Scottish Secondary Teachers Association called for a review of the approval process.
Alan McKenzie, acting general secretary, said: "It seems sensible to review the way this is working because approval has to be applied evenly. "If a Catholic school really needs a teacher in a specific subject they simply waive the requirement anyway and that is unfair on those who are subject to a much more rigorous process."
Gary McLelland, education officer for the Humanist Society Scotland, added: "The current system is not only an affront to equality and fairness, but we think Catholic schools are missing out by limiting their staff. The system of approval is discredited."
However, Michael McGrath, director of the Scottish Catholic Education Service, said the system worked well.
He said: "Like any system which relies on personal testimony and people giving references it is open to inconsistencies, but as a system it works fairly well. There is also an appeal system if people feel they have been refused approval on false grounds."
The right of approval, enshrined in the 1980 Education Act, seeks to establish the "religious belief and character" of teachers who want to work in Catholic schools.
The policy has created tensions in the past because of its apparent contradiction with employment regulations which make it unlawful for an employer to discriminate on the grounds of religion or belief.