Ninety-eight per cent of the estimated benefits of several high-profile National Programme for IT in the NHS programmes are yet to be realised, according to the National Audit Office.

However, the Department of Health believes that benefits will slightly exceed costs over the whole life of the systems implemented.

In a note for the Commons’ Public Accounts Committee, the NAO says 98% of estimated benefits of the London Programme for IT, the Southern Programme for IT and the Electronic Prescription Service and Summary Care Record programmes, were still to be realised at March 2012.

The note, which reports on a much-delayed review of the benefits of the programme demanded by the PAC when it investigated NPfIT in August 2011, says that in March 2012, the DH put the total cost of the programme at £7.3 billion.

It put the total benefits at that point at £3.7 billion. It estimated that by the end of the programme, the total costs would be £9.8 billion and the benefits £10.7 billion.

These figures do not include the costs and benefits of the programme in the North, Midlands and East of England, where CSC was contracted to deliver the Lorenzo electronic patient record, because of repeated contract negotiations in the region.

The NAO comments that because of these changes, which make the end point of the programme uncertain, and questions about whether systems can be effectively deployed on time, there is “very considerable uncertainty about whether the forecast benefits will be realised.”

In a statement, it explained: “Around two thirds (£6.5 billion) of the total estimated benefits are forecast to arise after March 2012. For three programmes, 98% of the total estimated benefits are still to be realised.

“There is a range of risks to the realisation of future benefits. In particular, for some programmes, future benefits rely on the successful deployment of a set number of systems at a set time.

“Experience over the past ten years suggests this will be challenging to achieve, particularly in the case of the local care records programme.”

The NAO note adds that the coalition government’s decision to effectively end NPfIT, and to split national responsibility for IT between the DH, NHS England, and the Health and Social Care Information Centre, is a further risk to achieving any benefits from what is left of the programme.

NPfIT was set up in 2002. It aimed to create a national infrastructure, some national systems – such as Choose and Book and the EPS– and an integrated care records service made up of two components – the SCR and local, detailed care records.

To create the latter, it placed contracts with local service providers to deliver ‘strategic’ systems to trusts. Three LSP areas remain – the South and London, where BT is deploying Cerner Millennium, and the NME.

Only a limited number of trusts received strategic systems, and the NAO concluded in its last report on the programme that it would never deliver the objectives set for it. This triggered the August 2011 PAC hearing that demanded the new benefits statement from the DH.

The note from the NAO says it was asked to review the statement ahead of its publication.

It says the DH seems to have taken a robust approach, although “it is not possible to compare the forecast benefits set out in the statement with what was expected at the outset of the national programme because the Department did not establish a comprehensive baseline.”

The DH appears to have identified a range of benefits, ranging from straightforward financial savings – “for example, reductions in the cost of storage and materials from switching to electronic x-rays and scans from using picture archiving and communications systems” – to less tangible improvements.

These include non-cash releasing savings for trusts – “for example, trust staff can be used on other tasks were care records systems to automatically construct discharge letters” – and for society as a whole – “for example, where patients spend less time chasing referrals [because of Choose and Book].”