Leading lawyers argue the provision is a "vital safeguard" for families that should be preserved.
The Faculty Of Advocates also warns the changes will allow education authorities to be the "final judge of their own alleged failures".
The warnings come after a Scottish Government consultation on changes to Section 70 of the 1980 Education (Scotland) Act. Under Section 70, parents or pupils can make a complaint directly to the Scottish Government about failures by their local education authority or school.
If the complaint is upheld, Scottish ministers can make an order through the Court Of Session holding councils to account.
However, under the new proposals, the complaint will be addressed to the Scottish Public Services Ombudsman, who does not have the same powers.
A consultation response from the Faculty said the rights of parents and pupils could be "severely undermined" if Section 70 were to be repealed. It added: "Section 70 provides a vital safeguard. It allows the ministers as an independent entity, appropriately advised by experts, to come in and examine what a local authority is doing and to support and enforce the rights of parents and pupils.
"It is a well-established safeguard, the removal of which has not been adequately argued for or justified."
The Faculty argued the provision had been a powerful tool for parents in recent years as new issues emerged in education, such as dyslexia. The submission added: "Local authorities themselves should not be the last resort provided for in statute for complaints whereby they are asked to judge their own failures.
"The existence of a last resort power means authorities will know they must comply with statutory duties."
Larry Flanagan, general secretary of teaching union the Educational Institute of Scotland, accused the Scottish Government of failing to consult with the teaching union on the issue. He added: "There may be a perception that having the Education Secretary as the final arbiter of a complaint against a local authority risks an element of the process being politicised.
"The use of the ombudsman as an alternative might avoid that difficulty, but it should be remembered the Cabinet Secretary does not only deal with complaints - he has the power to direct the Court Of Session and a council cannot disregard that. As we understand it, the ombudsman would not have similar powers."
A Scottish Government spokesman said the proposals would ensure complaints continued to be considered independently.
He said: "The ombudsman currently considers complaints where a member of the public claims to have suffered injustice or hardship as a result of maladministration or service failure in relation to public bodies or organisations providing public services.
"We are in the process of analysing consultation responses and will issue a response later this year."
A spokesman for the Convention Of Scottish Local Authorities, the umbrella body for councils, said it were unaware of concerns over the change.
He said: "As far as I understand this consultation has just closed, with no decisions yet being made.
"Regardless of the final mechanism, Scottish councils will continue to offer quality education provision to children and young people and will continue to engage constructively with pupils and parents in pursuit of this aim."