Christine Connelly, CIO at the Department of Health, is set to resign at the end of the month.

The news may mark a crisis for the failing £11.4 billion National Programme for IT, which has lost two of its lead suppliers, Accenture and Fujitsu, and has been heavily criticised over renegotiated, multibillion pound delayed work with remaining providers BT and CSC. The programme, centred around digital patient records, has also been unpopular among a number of doctors and patients.

Connelly was recently subjected to a tough grilling in parliament by the Public Accounts Committee, in which she gave most of the technical and financial answers to angry MPs. She sat alongside the National Programme’s senior responsible owner, NHS chief executive Sir David Nicholson, who was not immediately able to define how much time he spent on the project in an average week.

Connelly – an ex-CIO at Cadbury Schweppes and BP, who joined the NHS in September 2008 in an attempt to rescue the failing programme five years in – will be replaced on an interim basis by Katie Davis, an executive director at the Cabinet Office’s Efficiency and Reform Group.

The announcement follows plans by the Department of Health to cut the number of Director General posts. Connelly today said she would not apply for any of the changed posts.

“The Department of Health faces a major reorganisation of its top structures that will result in fewer Director General posts,” she said. “I have been reflecting on whether I would wish to go for one of those roles and decided that I will not.”

“I have had a fascinating and challenging time in this role and I have decided that this is the right time to step back and think about what I might do next.”

Connelly today expressed her confidence in the benefits of improved IT in the NHS, echoing comments she made to the Public Accounts Committee. "I believe that information and technology have the potential to dramatically change the way health services are delivered to patients, and we are already seeing this happen in many parts of the service. I am confident that informatics will have a major role to play in delivering both the quality and efficiency challenge that the NHS faces."

Health secretary Andrew Lansley, who recently branded the National Programme as an “expensive farce”, said Connelly had “brought a huge amount of experience, talent and technical knowledge to the National Programme for IT”.