Questions are being raised about the NHS's ability to push ahead with plans to close services.
Many local councils are using their powers to object and asking the health secretary to intervene.
In the last two years, 23 have referred NHS plans to the government, with ministers fully supporting the health service in only eight of these cases.
It comes as the government publishes a report calling on the NHS to improve its approach to reconfiguration.
Department of Health official Sir Ian Carruthers, who was acting chief executive of the NHS before David Nicholson took up the post in September, has been touring the country in the last few months talking to staff involved in reconfiguration.
His report is expected to call on NHS managers to engage better with doctors and spend more time consulting with local residents.
"Managers need to work closely with clinicians in presenting the case for change clearly and honestly to patients and the public"
Up to 60 NHS trusts are in the process of drawing up plans to strip some hospitals of key services, such as A&E and maternity services, and centralising them at super hospitals, while reshaping community services.
The proposals that have been put forward to date have prompted unprecedented opposition, with marches being organised up and down the country.
The dissatisfaction with the way the NHS has approached the issue can also be seen over the number of councils which have used their powers to try to influence decisions.
Where NHS bosses want to make significant changes to services, they need to consult councils.
And if local authorities are unhappy with the way consultations have been carried out or believe the plans are not in the interests of the health service, they can ask Health Secretary Patricia Hewitt to intervene.
The BBC has learned that in the last two years, 23 referrals have been made by councils to Ms Hewitt - 16 in the past 12 months alone.
She has fully supported the NHS on eight occasions and five cases have not yet been decided.
In the remaining 10 cases, the heath secretary has asked the health service to rethink its plans, sided with the council's protests or the local NHS has withdrawn the plans.
In one of the most recent cases, health officials on Teesside were told last year they could not go-ahead with plans to strip the University of North Tees hospital of services.
Accountability
A spokesman for the Local Government Association said: "It is a question of accountability. Councillors are accountable to the local community in a way that the NHS is not.
"They are the voice of the local people and I think this shows the NHS should be having a look at the way it is carrying out these consultations in some places."
Dr Gill Morgan, chief executive of the NHS Confederation, which represents NHS managers, conceded there was scope to improve the way reconfigurations had been handled.
"The point of reconfiguration is to improve the NHS for patients and get the best use of taxpayer's money.
"Managers need to work closely with clinicians in presenting the case for change clearly and honestly to patients and the public."
But a spokeswoman for the Department of Health said: "It should be remembered that NHS consultations or decisions that are referred to the health secretary are the ones which have not been agreed locally.
"Many more reach local consensus and are not referred to her."
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