Staff across the NHS should be able to access data under the scheme
It will be at least 2014 - four years later than planned - before a single NHS electronic patient records system is in place in England, say auditors.
The head of the National Audit Office, Tim Burr, said the challenge was "far greater than envisaged".
But an NAO report said the project was on budget and that staff thought it would improve patient care.
MP Edward Leigh, who chairs the Commons Public Accounts Committee, said further delays could damage public confidence.
The National Programme for IT in the NHS is one of the most ambitious computer projects ever undertaken - replacing hundreds of different computer systems spread across hospitals and GP practices with new, compatible versions that will allow NHS staff anywhere in England to access a patient's medical records.
However, the technical challenges involved have led to significant delays and some trusts, desperate to replace ageing systems in order to offer the government's "Choose and Book" service for patients, have been forced to install "interim" systems which will eventually have to be replaced again.
The NAO is responsible for the monitoring of public spending, and its latest report says the benefits are now starting to emerge.
It said that the fixed-price contracts used meant that their costs remained "broadly unchanged", despite the delays, but that it was likely to be 2014 or 2015 before every NHS trust was running the care records system.
Tim Burr, head of the NAO, said: "The challenge involved in delivering the National Programme for IT has proved to be far greater than envisaged at the start, with serious delays in delivering the new care records systems.
"Progress is being made, however, and financial savings and other benefits are beginning to emerge."
He said that the priority now was to finish developing and deploying the systems.
A spokesman for Connecting for Health, which is overseeing the project, said it "regretted" the delays.
He added: "The new IT systems in the NHS are on course to deliver better care and an estimated £1.14 billion in savings by 2014.
"The National Programme for IT has already delivered a total of £208 million in savings by providing quicker, more efficient and convenient patient care."
Others are less convinced by these timescales.
Tony Collins, who has investigated the project for the magazine Computer Weekly, said it was possible that some trusts might not want to run the systems offered to them.
"Ministers are discovering that an IT-based scheme conceived at the centre cannot be imposed on a devolved NHS - a lesson that should have been learned from failures in the 1990s."
Dr Chaand Nagpaul of the British Medical Association, said: "It is clear from this report that the setting of unrealistic deadlines has been very damaging.
"Slipping deadlines for new IT systems and the premature release of systems that are not fit for purpose has been deeply frustrating for NHS staff leaving many doctors thoroughly disillusioned with the programme. "
The report will be considered by the Commons Public Accounts Committee next month.
Mr Leigh said that confidence in the project had been "damaged" by "unrealistic expectations".
"The current timetables for the care records system to be fully deployed by 2014-15 had better be realistic.
"The Department of Health cannot afford further knocks to the programme's reputation or our confidence in it."