However, the third, a 9,000 home development east of Colchester, could still go ahead.
Mr Clews has said the councils behind the North Essex Garden Communities – Colchester, Tendring and Braintree – should remove the West Tey and west of Braintree garden communities from the joint section of their Local Plan to proceed.
In his letter to the authorities, he raised concerns over financial viability of both as well as the deliverability of the proposed Rapid Transit System linking them.
He said: “Even if the A120 dualling scheme has a good prospect of being delivered as part of the programme, not to provide the necessary public transport connections from these two garden communities would directly conflict advice the transport system needs to be balanced in favour of sustainable transport modes.
“I find that the proposed Colchester/Braintree borders and West of Braintree garden communities are not justified or deliverable.
“Consequently, the plan’s spatial strategy, and thus the plan itself as submitted, are unsound.”
However, Mr Clews said the financial viability of the third garden community, off the A134 near Greenstead and Wivenhoe, was “very strong”.
He has recommended two ways forward for the authorities – either withdraw the plan in its entirety, or consult on it again with two of the garden communities removed.
Mark Cory, leader of Colchester Council, said: “This decision is obviously a mixed bag for Colchester and north Essex as a whole and one that we will need to consider carefully both individually and collectively.
“This administration believes it is better to plan new developments to deliver infrastructure first, as the councils have been trying to do.
“Leaving it to developers to provide the necessary physical and social infrastructure is not good enough. The inspector does back our approach and has outlined a clear way ahead in his letter.”
Graham Butland, leader of Braintree Council, said: “Clearly the decision of the Inspector is a huge disappointment and one that will adversely impact on the district for years to come.
“I am proud that, together with Colchester and Tendring councils, we brought forward imaginative and far-sighted plans for meeting the housing needs of our communities both now and in the future.
“These plans would have fundamentally shifted the balance of decision making from developers to local communities.
“Unfortunately, the Inspector’s decision means that we will have to consider whether additional sites around our existing towns and villages for both the additional housing and for gypsy and traveller sites will now be required
“This is something we wished to avoid but unfortunately the concept of further urban sprawl is now a real threat.”
The authorities say they “remain committed to the principles that made the garden communities so beneficial to the community”.
Neil Stock OBE, Leader of Tendring Council, said: “We welcome the scrutiny given by the Inspector to our proposals, and while it is a shame that he does not find all of the proposed garden communities viable at this time it is good that he recognises our high standards and approves the garden community method.
“It is also a clear mandate for the Tendring/Colchester Borders project, and we will continue to work with our strategic partners to deliver both sections of our Local Plan.”
A Ministry of Housing Communities and Local Government spokesperson said: “The Government is working hand-in-hand with local communities to deliver much-needed new homes across the country.
“We remain committed to supporting new garden communities and helping these schemes to get off the ground.”