The health service should learn from past government IT projects where poor user consultation has contributed to failure, said John Powell, who chairs the committee.
The programme aims to allow all GPs in England to book hospital appointments for their patients online. It will also create about 50 million electronic health records and allow the electronic transfer of prescriptions.
But Powell said the programme had not done enough to involve the medical profession in the design and implementation of new systems.
"The programme should support healthcare workers in delivering a better service to their patients. We hope that improvements to IT systems will reduce the administrative burden on doctors so they can spend more time treating patients," he said.
"This goal will only be realised if the national programme can provide systems that are at least as effective as those currently in use.
"There is no point investing billions of pounds in systems that do not have the confidence of users," Powell added.
A spokesman for the national programme said, "We know that engaging with the clinicians who will use new IT systems is vital. We know there is more work to do and we are confident that we will build momentum."
The national programme had consulted thousands of doctors and nurses about its work, the spokesman added. "We are also strengthening the arrangements for clinical engagement, building a team of health professionals."