Announcing the shock departure, NHSIA chairman Professor Alastair Bellingham said Bell had, "not been able to give a commitment to remain with the organisation over the next two years to lead it through the next phase of development and delivery."
"In those circumstances," he added, "We have agreed that his immediate departure is the best means of achieving the stability and progress that we all seek. We wish him well in his future career."
The NHSIA is charged with delivering the national IT components for the government's drive to modernise the health service. Bell welded the NHSIA into a strong single unit from a group of disparate organisations.
In a statement Bell said: " [Unifying the NHSIA] is the challenge for which I was recruited. As it has neared completion, I have been discussing my future plans with the Board. I now feel that the time is right to move on and I wish the NHS Information Authority well in future development."
Appointed in August 1999, Bell quickly took some hard decisions. He scrapped a politically convenient target of getting every computerised GP's surgery on to NHSnet by the end of the year. The target was, he said, "unachievable".
He then set about negotiating a new service level agreement with NHSNet service providers BT and Cable & Wireless. This brought considerable improvements to the troubled service.
Other notable achievements include the creation of NHS.UK, a portal for NHS practitioners.
Bell wanted to improve the morale of NHS IT professionals. He called for the NHS to pay the market rate for the job and spoke earnestly about creating a community of IT practitioners who could pool knowledge and best practice.
He also wanted to ensure the NHS got value for money from its suppliers, calling for a more evolutionary approach to IT projects and the purchase of fewer bespoke systems.
Bell leaves as the NHS is embarking on some of its biggest ever projects, including the £300m human resources/payroll system that will cover the entire health service, the implementation of a public key infrastructure security system and the retendering of the NHSnet contract.
Deputy chief executive Gwyn Thomas will take over in an acting capacity with effect from 30 September.