Britain's highest paid civil servant has announced his resignation as head of the £12 billion computer project for the National Health Service.

Richard Granger, 42, chief executive of NHS Connecting for Health, was responsible for upgrading information technology (IT) systems and introducing electronic patient records. Although computer systems have been improved in many trusts, the project has been criticised for delays and design flaws.

The departure of Granger, who was paid £290,000 a year, will be seen as a further setback for the project. He has been credited with updating hospital IT systems from “the stone age” and ensuring that private contractors involved in the project were not rewarded for failure.

Granger will leave in the next few months and said he was considering offers to return to the private sector. “I passionately believe the programme will deliver ever greater levels of benefit to patients over the coming years,” he said.

The NHS project, the biggest civilian computer project, was backed by Tony Blair to deliver detailed electronic records for every NHS patient. The electronic record system is now more than two years late and Gordon Brown is expected to review its progress when he becomes prime minister.

Tony Collins, executive editor of Computer Weekly, the industry magazine, which has called for an independent inquiry into the project, said: “Without Granger the risk is that this programme will now fall apart. The programme has highlighted the need for proper electronic records in the NHS, but you have to ask what it has achieved that trusts could not have done on their own. It has also not delivered on the main objective of a centralised patient record system.”

Granger was appointed head of the project in 2002 after successfully managing the introduction of the IT element of the congestion charge in London.

Confronted with what he saw as the intransigence of the medical profession and the determination of IT suppliers to make high profits at the taxpayers’ expense whatever their performance, Granger tried to introduce a tough competitive climate for the contractors.

His metaphor for the project was a sledge being pulled by huskies. Those who fell by the wayside would be “chopped up and fed to the other dogs” to ensure that those who survived worked harder.

The former management consultant was respected by many in the industry but others were taken aback by his abrasive and demanding approach. One contemporary once described working with him as a “deeply corrosive experience”.

Connecting for Health proved to be a huge challenge as NHS staff complained they had not been properly consulted and experts argued it was foolhardy to keep patient records in one central database, warning the system might be vulnerable to unauthorised users.

Some of the most stringent security measures in the IT industry have been devised to protect confidential information and patients can also opt out of their records being uploaded.

To add to Granger’s woes, the contractors tasked with developing the computer technology were hit by problems. Last year Accenture, the consulting and technology company, withdrew from the programme and iSoft, one of the programme’s software suppliers, is being investigated for alleged accounting irregularities.

Granger will point to systems in the project which he believes have been successful. These include the “choose and book” scheme, under which patients can choose a hospital for treatment while at the GP’s surgery.

Norman Lamb, the Liberal Democrat MP, said: “This is a grandiose scheme but it was not properly defined at the start. It is costing billions of pounds and we need to make sure that we are not building something that isn’t fit for purpose.”

Granger’s resignation has surprised many in the industry. Last weekend he gave an interview in which it was said he was keen to steer the project to “calmer waters”.

Dr Simon Eccles, the project’s national clinical lead for hospital doctors, said: “He is going to be a hard man to replace. He has brought a unique set of skills to the programme. If this had been delivered by the NHS the budgets would have been bigger and the delays would have been greater.”

Lord Hunt, the health minister, said the IT programme would not be adversely affected by Granger’s departure. “The NHS IT programme will provide safer, faster and more efficient healthcare for patients,” he said.

“It is already being used by clinicians and bringing benefits for patients with digital technology, transforming diagnosis and treatment every day.”

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