A flagship government scheme to introduce electronic medical records for all patients as part of its NHS reforms is running at least two years behind schedule, health minister Lord Warner said today.

The minister responsible for the health service's National Programme for IT also admitted the full cost of the programme was likely to be more than three times the widely quoted figure of £6.2bn. The new IT network is pivotal to modernising the NHS, and the delay represents a further blow to the government's health reforms.

The government awarded the 10-year £6.2bn contract to Isoft and other companies to set up electronic patient records that can be accessed by authorised NHS professionals across the country.

The IT programme is also designed to allow outpatient bookings to be made online, prescriptions to be transmitted electronically, and to exchange old-fashioned film for x-rays and scans with digital images.

Speaking ahead of a report due next month by the National Audit Office on the progress of the IT project to date, Lord Warner sought to clarify the full cost of the project being introduced as part of the patient choice agenda.

In an interview with the Financial Times today, Lord Warner conceded that the £6.2bn only covered the national contracts for the systems' basic infrastructure and software, with the full cost of training staff, buying computers and assimilating existing systems nearing the £20bn mark.

Delays in providing the software meant the system would not be in place until early 2008, knocking back the original deadline for the end of this year by at least two years.

The plans have also been stalled as a result of arguments with the medical profession over what should be included on the national medical record, and how patients' data should be added.

Lord Warner told the FT today that some parts of the programme "are going pretty well and pretty much on time", while others "are going more slowly than we would otherwise like".

The government has had to "regroup" over the national summary record, which make patients' data available "wherever and whenever" they are needed.

The head of the NAO, Sir John Bourne, criticised the Department of Health in January over its failure to engage doctors in preparation for the new system until they could be demonstrated to work without glitches.

A new electronic booking system, allowing GPs and patients to fix an appointment at the most appropriate hospital, was supposed to be working everywhere in England by the end of this year. But by December 2005, only 63 bookings for outpatient appointments had been made online by GPs, against a target of 250,000.

A GP survey carried out in February by medical pollsters Medix revealed massive disillusionment with the programme among doctors.

Only one in five (21%) expressed enthusiasm for the new system, down from over one in two (56%) the year before.

Concerns include confidentiality of patient data put online, and the extended doctor-patient consultation sessions needed to exercise the choose-and-book system, whereby patients are given choice of treatment from a range of hospitals.

The BMA has called for explicit patient consent before any details are put on line.

Lord Warner told the FT that many in the medical profession supported comprehensive medical records on line.

"The medical profession have to come together" to agree on what data will be included and how they are added, he said.

Dr Hamish Meldrum, chairman of the BMA's GPs committee said GPs were anxious to see that their various concerns were addressed before the scheme was rolled out.

"Family doctors have been in the forefront of using modern technology but have been concerned that this national scheme for an electronic database of patient information is trying to do too much too quickly and could threaten patient confidentiality.

"The BMA's GPs committee position is that patients should be given the opportunity to provide an informed consent before their health record details are put on a national database. This is particularly important as there is so much uncertainty and a lack of public information at the moment."

The Conservative party said the delay in rolling out the new IT system signified a "disturbing" indicator of failure.

The shadow health secretary, Andrew Lansley, called on the government to review the programme before it collapsed.

"It is not too late to offer greater opportunities for trusts and GPs to have more freedom to buy equipment and software of their choice, which is system-compliant", he said.

"It not too late to secure confidentiality by holding data in local servers rather than a central server, and it is not too late for patients to have an NHS card, which would enable patients to govern the release of data when they are present and give them control over access to their record.

"I urge the government to open up the programme to review and, if necessary to change before the project is driven to collapse."