The National Audit Office pointed to "serious delays" in applying new software for the National Programme for IT in the NHS and said the Government had underestimated the challenges involved.

In a progress report, the NAO concluded that while all elements of the £12.7 billion programme are advancing and some are complete, the original timescales for the Care Records Service - one of the central processes - were "unachievable, raised unrealistic expectations and put confidence in the programme at risk".

In particular, the software planned for the North, Midlands and East areas, called Lorenzo, has taken much longer than planned, forcing some trusts to take an interim system, the report found.

The IT programme involves four main projects: a centralised electronic medical record system for 50 million patients; an online "choose and book" system for booking hospital appointments - deployment of which, according to today's report, is nearly complete; electronic prescriptions; and fast network links between NHS organisations.

It is expected to link more than 30,000 GPs in England to almost 300 hospitals.

But it has come in for repeated criticism, including from committees of MPs, over the delays as well as fears over the security of patient information.

Tim Burr, head of the National Audit Office, said: "The scale of 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.

"The priority now is to finish developing and deploying care records systems that will help NHS Trusts to achieve the Programme's intended benefits of improved services and better patient care."