The government has buried its response to a damning report by MPs on the NHS’s £12.4bn National Programme for IT (NPfIT) in a set of Treasury minutes.

The document, slipped out just before the parliamentary recess, includes a pledge to produce a first annual statement of the costs and benefits of the huge computer project later this year.

In April, the powerful Commons Public Accounts Committee warned that NPfIT was unlikely to deliver significant benefits to the treatment of patients by the end of its 10-year contract without a fundamental change in the rate of progress on the project.

Responses to Parliamentary Select Committee reports are usually published on the committee’s web page. But at the time of writing the document was not available through this channel and spokespeople for the Department of Health and NHS Connecting for Health – the agency that runs NPfIT – could not confirm whether it had been published.

The Public Accounts Committee warned that the Department of Health was “unlikely to complete the programme anywhere near its original schedule”, noting that, four years in, there was still uncertainty about the costs and benefits of the scheme.

If the project fails, “it could set back IT developments in the NHS for years, and divert money and staff time from front line patient services”, the committee report said.

But the government has rejected the MPs’ call for an independent assessment of the business case for NPfIT in the light of progress and experience made so far.

The response says: “The intention is to include details of both the financial and non-financial benefits within the annual statement of benefits realised.”

The government “does not consider there are grounds for an independent review of the business case at this stage”.

The response says the government “accepts the general principle” of a recommendation to set out which elements of functionality originally contracted for under NPfIT would be available for implementation by the end of the 10-year period and to prioritise deployment of the systems that benefit the NHS most.

“Work is underway with the NHS to determine its priorities. The results will be provided to the Local Service Providers and plans will be adjusted as required,” it says.

But ministers have rejected the MPs’ calls – sparked by concerns that NPfIT suppliers such as the troubled iSoft were running late in delivering key components of the scheme – to modify the procurement process to let NHS trusts select from a wider range of patient administration and clinical systems.

The response says: “Centralised procurement, through a small number of suppliers, was a key feature of the procurement process so as to avoid the disadvantages, and the expense, of the haphazard approach of the past.”

Although there are just two suppliers of the crucial acute patient administration systems, “many more suppliers are contracted across the programme as a whole”, it adds.

A procurement exercise to increase the number of potential suppliers has brought expressions of interest from 221 suppliers, with 111 of these “longlisted” so far.

“The intention is to award a series of framework contracts to selected suppliers who can then compete for subsequent business if the need arises,” the government response says.

The framework contracts would be “complementary to the existing suite of Programme contracts and provide contingency”.

Ministers rejected the call for an independent review of the performance of NPfIT’s lead contractors. “It is better to target reviews at individual problems,” the response document says.

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Government defends £12.4bn NHS IT scheme after MPs' damning report