With the NHS bill receiving royal assent, a leaked document drawn up by senior civil servants warns that the government's reforms could damage the health service.
The draft risk register, written by staff at the Department of Health, said there is a danger that "the NHS role in emergency preparedness/responsiveness is more difficult to manage through a more develoved organisation, and so emergencies are less well managed/mitigated".
The document was leaked to the NHS analyst Roy Lilley, who told Channel 4 News: "Given the importance the NHS has in the management of emergencies - imagine another London bombing or something going catastrophically wrong with the Olympics - that worries me."
The paper says costs could rise under the new NHS if GPs make greater use of the private sector. It warns that implementation of the reforms could proceed "before adequate planning" has been carried out and argues that control of spending could be "lost due to the restructuring of budgets".
The draft risk register was drawn up in September 2010. It appears to be an earlier version of a document whose publication the Labour Party has been demanding.
Last week, Labour tried to halt the final passage of the bill in the Commons unless the government agreed to publication. It lost the vote and the legislation is expected to receive the Queen's signature on Tuesday.
David Cameron will never be forgiven for knowingly taking these risks with the country's best-loved institution. Andy Burnham, shadow health secretary
Shadow health secretary, Andy Burnham, said: "Now we know why David Cameron refused to publish the risk register before the bill was through parliament. It's because civil servants were telling him his reorganisation was likely to cause major damage to the NHS. David Cameron will never be forgiven for knowingly taking these risks with the country's best-loved institution."
Health Minister Simon Burns told the Commons on Tuesday: "Ministers do not comment on leaked documents." Health Secretary Andrew Lansley told the Commons on 20 March that risk registers looked at worst-case scenarios.
The information commissioner has ruled the latest risk register should be released, and a tribunal upheld the decision after an appeal by the government to block its publication.
It could be argued that as changes have been made to the bill since September 2010, there is less risk of problems occurring.
But Mr Lilley, a former NHS trust chairman who edits the nhsManagers.net website, told Channel 4 News: "The question is what has changed and what risks have been anticipated and the answer is not very much."
Labour has seen more recent NHS risk registers which it says repeat the concerns raised in the draft.
The draft document uses traffic light signals to flag up areas of concern. "I've seen a lot of risk registers," Mr Lilley said. "They come in green, amber and red, and what struck me immediately was the extent to which it is all red. There's a strong risk this will grind to a halt and will not work. It's the system design that worries me."
The bill, which devolves 60 per cent of the NHS budget in England to GPs, is opposed by the British Medical Association, Royal College of Nursing, Royal College of GPs, Royal College of Midwives and the Faculty of Public Health.
It endured a tortuous journey through parliament. To appease his Liberal Democrat coalition partners, David Cameron agreed to a pause in its passage and further consultation.
Professor Steve Field was asked to liaise with doctors, nurses and other NHS professionals and develop proposals to improve the bill. The government accepted the recommendations of the NHS Future Forum, chaired by Professor Field.