The troubled multi-billion-pound NHS computer system suffered a fresh blow last night when it emerged that two-thirds of the hospital trusts due to have installed an electronic patient administration system for booking appointments with consultants by the end of October will not meet the deadline.

The delay has raised concern that the project - already two years behind schedule - may be continuing to overrun. The government believes it will cost £12.4bn but critics fear more delays could mean costs spiralling to more than £15bn.

Of the 22 NHS acute trusts supposed to be receiving the new patient administration system by the end of October only seven believe they will now hit the target, according to a survey by E-Health Insider, a specialist online magazine for health professionals. The system is crucial to the entire project as it is the foundation on which all other aspects of the IT system are built.

The revelation of the difficulties undermines the credibility of claims made by Connecting for Health, the government body overseeing the project. In June it told MPs on the influential Commons Public Accounts Committee that 22 trusts would get replacement systems by the end of next month.

Two committee members, Richard Bacon, the Conservative MP for South Norfolk, and John Pugh, Liberal Democrat MP for Southport, have taken the unprecedented decision of warning that the NHS is in danger of 'sleepwalking to disaster' and wasting billions of pounds on the project unless it is dramatically scaled back.

The upgrade of NHS computers, the largest IT project in the world, has been dogged by controversy and criticised for over-centralisation. Its largest software supplier, iSoft, is under investigation by the Financial Services Authority for possible accounting irregularities.