Under Assembly government guidelines, if a parent or other person makes an official complaint about a whole governing body, the clerk must immediately notify the headteacher and the local authority.
The authority can issue a warning notice if it thinks the governing body is causing concern, or it can ask the governors if they want the complaint heard by an independent committee.
But the governors have the right to refuse this and can opt to deal with the complaint themselves, retaining the power to take evidence from witnesses and make their own decision.
Now several members of support body Governors Wales have called for the Assembly government to revise the system so such grievances are dealt with independently.
Members were shocked to discover the guidelines during a workshop at the organisation's annual conference recently.
One member, who refused to be named, said: "If this ever happened, we could be accused of a whitewash. It's farcical."
Kath Roberts-Jones, chairwoman of governors at Brynllywarch Hall, a residential special school in Powys, said: "This has got to be addressed; it's not fair to governors. I don't know how you can be objective enough in that situation to decide something like that.
"I suppose it would depend on what the incident was, but there could be a conflict of interest. Even if you have no case to answer, the person who's got the complaint will think you have."
Ms Roberts-Jones, who is also a Powys county councillor, said it should be the job of another governing body or an independent panel to hear the complaint.
The chairman of governors at one Powys primary school, who also refused to be named, has encountered such a situation at his school.
He said: "Governing bodies need to be transparent and open to scrutiny. If a layperson looked at this rule, they would see it is nonsense. In these cases the local authority needs to step in and allocate complaints to an independent body."
Steve Gullick, director at the All Wales Centre for Governor Training and Research, who gave the workshop, called the situation an "anomaly".
He said: "This doesn't happen very often. In any cases I have come across, the governors have accepted an independent committee. But the bottom line is they don't have to, and that seems illogical to me. If this can be changed, I think it would be worth looking at."
Jane Morris, director of Governors Wales, said: "We are mindful of the concerns from some of our members and will seek to discuss them with the Assembly government in a meeting in the new term."
The advised course of action was originally laid out in a circular distributed by the Assembly government in 2004.
A spokeswoman said the government is currently updating the advice and taking into account the views of various bodies, including Governors Wales.
"The new guidance will be published in due course," she added.