Glasgow City Council and North Lanarkshire Council have both attacked ministers' plans, suggesting the measures demonstrate interference in local democracy from central government.
The row has blown up over proposed amendments affecting the Schools (Consultation) (Scotland) Act 2010.
Loading article content
Key proposals include a new presumption against the closure of rural schools and an emphasis on councils having to show the educational benefit to pupils when a school is closing.
The Scottish Government has also suggested setting up an independent appeals process for parents unhappy with a council decision.
A five-year moratorium could also be introduced to prevent local authorities returning to close a school that has been saved.
The submission from North Lanarkshire, to a consultation that closed on September 2, says the council believes provision of education "is primarily a responsibility of democratically elected local councils".
It states: "As such local authorities should be empowered to manage their estate fully and will be held to account by their electorate in this regard."
The council goes on to say it is not convinced the proposals for an independent review of decisions will make the process any better.
North Lanarkshire also argues it should be acceptable for councils to conclude that the educational impact of any closure proposal is neutral, rather than improving education.
The submission from Glasgow agrees, describing the inclusion as unfortunate. It states: "In terms of absolute transparency it is critical that local authorities are able to put forward the economic arguments for school closure proposals, particularly in terms of how they may impact on other aspects of education service delivery or other local authority service delivery."
An independent referral mechanism would "introduce another tier of bureaucracy within an already over complex and time-consuming system", the council adds.
However, Sandy Longmuir, spokesman for the Scottish Rural Schools Network, said it was proper for central government to have an overview of local government decisions. He said: "Mistakes are often made. It is vital parents have an independent process that can hold councils to account."
Education Secretary Michael Russell said: "School closures are an emotive issue for all communities and it is important that they are dealt with in an open, effective and transparent manner."