The chief executive of the NHS today warned that the Government’s altered health reforms could create “the greatest quango in the sky” unless local GPs are quick to take responsibility for commissioning care for their patients.

The stark warning from Sir David Nicholson underlines growing concerns from some in the NHS that the changes to the Government’s health reforms announced earlier this week could have unintended consequences.

The editor of the respected Health Service Journal wrote that the reforms would result in the continuing “planning blight” that has afflicted the health service since changes were announced.

“This blight will distract and confuse. Quality will suffer, as will efficiency – despite the efforts of NHS staff to compensate,” he wrote.

Speaking to health professionals in London Sir David, who will head up a new national Commissioning Board to support local commissioning consortia said he was aware of criticisms that this would create a massive centralisation of budgets in a single organisation – because it will hold budgets where local groups are not ready.

“The NHS Commissioning Board could become the greatest quango in the sky we have seen,” he said.

“It needs to have clinicians at its heart and it needs to make sure the power house for change is the clinical commissioning groups. Our ambition must be to cover the whole country – this is something we need to make happen. My job is to make (the local clinical commissioning bodies) the best they can possibly be – I don’t want to make them jump over hoops.”

Sir David stressed that reform would need to have the support of medical workers across the country.

“One of the conditions we will find undoubtedly as we work through the changes, the challenges to the NHS is it will involve significant service change across the NHS," he said.

“One of the things that we know, in order to make that change happen is it has to have the confidence of clinicians across the whole system.”

But there were early signs that doctors who have already set up commissioning groups are disillusioned by the changes to announced by the Government – in particular the requirement that they should have representatives from hospital doctors outside their catchment are on their boards.

But Dr Roger Pinnock, chairman of the Ashford Locality Commissioning Group, said: ‘We’re in East Kent, we are effectively a peninsula. Where on earth is this consultant going to come from?’

Dr Chris Trzcinski, chairman of North and West Leicestershire consortia added: “People that want to be involved are the local consultants. You will end up with people who aren't directly involved in the local health service.”

Meanwhile the former health secretary Alan Milburn described the watered down reforms as the "biggest car crash" in the history of the health service.

Milburn – who is currently advising David Cameron on social mobility – said taxpayers faced writing "a very large cheque" as billions of pounds in efficiency savings would not be achieved as a result of "the screech of skidding tyres" caused by the government's U-turn.

"Many in both camps inside the coalition consider the U-turn a triumph. But it has the makings of a policy disaster for the NHS and, maybe in time, a political disaster for the government.”

He described the new policy as the "biggest nationalisation since Nye Bevan created the NHS in 1948", saying Cameron had handed over control to "the daddy of all quangos", the NHS Commissioning Board.

The ex-cabinet minister said scrapping the 2013 deadline for giving GP consortiums control of commissioning would result in a “patchwork of decision-making for years to come”.

Turning to the need to make £20bn of efficiency savings, he asked: "So how will the NHS books be balanced? By the usual device which policymakers have deployed every decade or so in the NHS: A very large cheque.

“It was precisely the situation David Cameron and George Osborne were trying to avoid. Sorry, George, but the cash you were saving in your pre-election budget for tax cuts will now have to be spent on a bailout for the health service.”

The Government's proposed changes to the controversial health reforms will be sent back to a committee of MPs next week.

MPs will debate a motion to recommit parts of the Health and Social Care Bill on June 21.