Children should be disciplined if they make false or malicious allegations against teachers, according to the Assembly government.
The stance, expected to appear in new guidance for schools on how to handle complaints made by pupils, has been welcomed by teacher unions.
But Peter Clarke, Wales's children's commissioner, fears the draft guidance could discourage pupils from raising real concerns.
In a report to last week's education committee, education and lifelong learning minister Jane Davidson told Assembly members that pupils should have "confidence that they will be heard if they raise a complaint, that it will be taken seriously and they will be treated fairly".
But draft guidance, due out for consultation later this month, also recognises the "very real issue" of pupils making false or malicious complaints.
"It advises that governing bodies need to send a clear message to pupils that raising a complaint is a serious matter and that they need to be truthful and honest," Ms Davidson said in her report.
"Pupils need to understand that false and malicious complaints are distressing and potentially damaging to those accused. They need to know a false allegation may lead to disciplinary action against the pupil making it."
Geraint Davies, secretary of the National Association of Schoolmasters Union of Women Teachers, welcomed the minister's comments and the proposed guidance, saying they were well overdue.
Brian Rowlands, secretary of the Secondary Heads' Association Cymru, said:
"Children must have the right to complain and we support that totally. But there must be a balance with false allegations."
Anna Brychan, director of the National Association of Head Teachers Cymru, said: "It cannot be right that a school leader can find their personal and professional lives blighted by malicious allegations while the pupil responsible faces no sanction. Protecting pupils' welfare must come first but rights come with responsibilities."
However, Mr Clarke insisted children should not be punished for claims that, on investigation, prove to be unsubstantiated. The Assembly guidance will need to distinguish carefully between such claims and clear cases where children have acted maliciously.
He cited an example of a fracas in a school corridor, in which a teacher intervenes to break up a fight. A child involved might rightly complain of being roughly handled, but this would constitute neither maliciousness on their part nor abuse by the teacher.
Mr Clarke added: "If a child makes a truly malicious complaint there needs to be repercussions. But there is a failure to distinguish between that and when something is not proven to be abuse. If this is publicised strongly, pupils will be put off because they will fear the consequences."
In his Clywch inquiry last summer, Mr Clarke found that pupils at Ysgol Gyfun Rhydfelen, Pontypridd, who complained of sexual abuse by drama teacher John Owen, were ignored. Owen committed suicide in 2001 after being charged with serious offences, 10 years after leaving the school.
Last month, Iwan Rees, a former Welsh teacher at John Beddoes secondary school in Presteigne, Powys, won pound;22,000 compensation from the county council. An employment tribunal ruled he had been unfairly dismissed in 2002 after two girls accused him of touching and trying to kiss them, despite police concluding that there were no grounds for prosecution.