Judge Justice Collins ruled in favour of an application for judicial review from lobby group Better Access Responsible Development on the grounds that the programme is undemocratic because local people have not been consulted and alternatives have not been considered.
The review will investigate whether the Government can legally impose eco-towns on local authorities and then act as the ultimate arbiter in a planning application without being biased. It could rule that the policy will have to be fully consulted and debated locally before it can be imposed on local authorities.
"I note there must be concern that the defendant [Communities and Local Government Secretary Hazel Blears] may have disqualified herself from considering any planning application for an eco-town because of perceived bias in its favour," said Justice Collins.
The review is expected to take up to a year.
Business lawyer LG's planning partner Stephen Turnbull said: "The deliverability of the Government's flagship policy is in doubt."
He added: "The Government is shortly due to issue its much-heralded Planning Policy Statement which is intended to, amongst other things, articulate its own policy, which local authorities then have to adhere to. It is difficult to see how this can be done with credibility whilst the judicial review process goes on."
The Department for Communities and Local Government pledged to continue with the programme.
"We believe we have acted properly throughout this process and will defend this claim vigorously," said a spokesman.