The programme aims to improve the quality of service and is expected to cost £12.4 billion over ten years to 2013-14. Part of the project, the NHS care records service, will replace local systems and make key information available electronically throughout England.
A number of clinicians have expressed concern about this system; last year a survey found a number of GPs did not support it.
After analysing elements of the IT programme and quizzing experts and the Department of Health, the PAC study found a number of other areas for concern.
These include a delay in the timetable (the piloting and deployment of the shared electronic patient clinical record is running two years behind schedule); suppliers to the programme struggling to deliver; and uncertainty about the costs of the scheme.
It adds that the Department of Health (DoH) also has to work hard to win the support of clinicians, supply solutions that are fit for purpose and win the respect of the workforce.
"There is a question mark hanging over the National Programme for IT…[it] is not looking good," said PAC chairman Edward Leigh.
"The leaders of the programme have talked long and loud about the benefits which it will bring to the NHS. The time for talking has ended. Resolute action at this stage by the leaders of the programme can do much to diminish the risks. The department must get a grip on what it and the NHS are spending."
But responding to the report, health minister Lord Hunt said that it was based on a study by the National Audit Office that is now a year out of date.
"Since then substantial progress has been made and the NAO recommendations have already been acted on. Costs of the programme have not escalated. In fact, the NAO acknowledged that costs were under control and the strength of the contracts means that payment is not made until systems are delivered which protects the taxpayer," Lord Hunt said.
"The NHS IT programme will provide safer, faster and more efficient healthcare for patients, and we do not underestimate the challenges of delivering a system of this size and complexity. Working with the NHS and clinicians, we are on track to meet our broad targets and, as the NAO confirmed, well placed to deliver this exciting project.
"When completed it will connect more than 117,000 doctors, 397,500 nurses and 128,000 scientists and therapists - bringing benefits to 50 million patients."
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