Key parts of the £6.8bn NHS IT upgrade in England are falling behind schedule, a funding watchdog says.
GPs have concerns about some parts of the new system
The National Audit Office said it was too early to tell if it gave value for money, but significant challenges remained if it was to be completed.
The watchdog said the online booking system and electronic care records were delayed and there had been a lack of engagement with clinicians.
Ministers said there were problems, but added the 10-year plan was on track.
The programme, run by a government agency called NHS Connecting for Health, is aimed at linking more than 30,000 GPs to nearly 300 hospitals by 2014.
The new systems include an online booking system, a centralised medical records system for 50m patients, e-prescriptions and fast computer network links between NHS organisations.
The NAO said that the total IT bill was set to be £12.4bn.
This includes the original £6.2bn cost of contract, which has now risen to £6.8bn due to the scope of the programme extending, and various other costs incurred from training people and paying for NHS trusts to implement the new systems.
The widely reported £20bn figure includes spending on the existing IT network while the new system is put in place.
The online booking system, Choose and Book, is already a year behind schedule, while the electronic records system has been delayed by more than two years.
The NAO report said that, while the costs of delays were being borne by private sector companies contracted to provide services, their impact could dent confidence in the programme.
KEY PARTS OF NHS IT UPGRADE
Choose and book - A system to allow patients to book hospital appointments at a place, date and time of their convenience from GP surgeries. Nearly 10m such referrals are made each year
NHS care records service - An electronic database of patient medical records which will allow NHS staff across the country to access information wherever someone is treated
Electronic prescriptions - More than 325m prescriptions are made each year. By 2007 the paper based system will be replaced with an electronic version, which will allow patients to pick up repeat prescriptions from any pharmacy in the country
It also said NHS staff did not feel involved in the implementation of the programme - with three out of 10 unaware it was happening.
Richard Vautrey, the IT lead on the British Medical Association's GPs committee, said the introduction of the system was "stuttering".
He added: "We still have serious concerns about patient confidentiality.
"But it is just one of many problems. IT systems on this scale are always going to run into problems.
"The problem is that politicians have raised the public's expectations by insisting on an unrealistic timetable."
'Getting to grips'
Edward Leigh MP, chairman of the Commons Public Accounts committee said: "Many staff, including GPs, are alarmed and dispirited by having the new systems imposed by diktat from above.
"They are also often confused about what the new systems are going to do and when. At the moment the jury is out."
Nigel Edwards, policy director of the NHS Confederation, told BBC News the project was in fact "largely on budget".
"This impression of an absolutely eye-wateringly large overspend is probably slightly incorrect.
"There's a degree of anxiety because, while the procurement was done really rather well, not enough attention was paid initially to really involving frontline clinical staff in finding out what they wanted and bringing them along with the programme."
Health Minister Lord Warner said: "The project has made significant progress, but there are some areas where we could make further progress.
"In hindsight, there was more we could have done in consultation [with clinicians].
"But I would stake my reputation that in the long term, this project will pay for itself."
Shadow Minister for Health Stephen O'Brien said the report shed light on the delayed and "ill-planned" NHS IT programme which the government had "constantly tried to shield from public scrutiny".