Ministers are using a new planning policy statement, to be published later in the summer, to set out the standards and potential locations for the environmentally sustainable new settlements.
But lawyers engaged by the Local Government Association said the proposals go against the principle of the current system of development through plans drawn up by local authorities, and could be open to legal challenge.
John Steel QC and James Strachan also said an existing PPS covered the concept of providing housing in new settlements in an environmentally sustainable way.
As a result, there did not seem to be any justification for promoting eco-towns outside the existing rules, "other than the Government's wish to avoid the system due to the proper need for scrutiny, which takes time", they said.
The LGA said the legal advice showed the Government's approach to ecotowns was "deeply flawed".
The Association's chairman Sir Simon Milton said the LGA was not opposed to the eco-towns as a way of meeting housing needs and combating climate change.
But he said there were concerns the current proposals would bypass local planning processes to impose the schemes on the public and councils.
He urged: "Ministers must talk to council leaders about adopting a new approach that will deliver development in places where councils and local people agree that eco-towns can work.
"Eco-towns must be delivered without bypassing the planning processes and ensure that new developments have good transport connections alongside the schools, health and leisure facilities which are needed to create places where people would want to live."
The Government, which shortlisted 15 proposals for the new settlements in April, has said up to 10 final approved bids would have to go through the planning process once they have been chosen later this year.
Bidders for eco-towns at Manby, Lincolnshire, and Curborough, Staffordshire, have pulled out, while part of a third bid, New Marston, Bedfordshire, has also been withdrawn.
A spokesman for the Department for Communities and Local Government said: "We absolutely disagree with the LGA's claims and believe this legal advice can only have been obtained on the basis of a misrepresentation of our policy.
"We have made it absolutely clear throughout that eco-towns will be different and will have higher environmental standards than a normal development and the applications will also have to be considered through the normal planning process."