Of the GPs and hospital doctors questioned, 31% were "unconfident", and 46% were "very unconfident" that the programme could avoid the difficulties and failures that have dogged other government IT projects.
The survey was commissioned by BBC Radio 4's File On 4 for a programme made in collaboration with Computer Weekly.
Glyn Hayes, former GP and chairman of the BCS' health informatics committee, said lack of consultation was a threat to the programme's success. "It is all very well consulting chief executives and strategic health authorities, but it does not trickle down to the people affected," he said.
Telecoms firm Cable & Wireless had to withdraw an NHS e-mail system it was taking over from EDS hours after it was introduced as a result of problems with the speed of data migration.
C&W and the national programme for IT said the problem meant that it was unlikely the migration could be completed in the allocated time because of the potential for lost data.
C&W stopped the migration and rolled back to the EDS service, the statement said. The service to NHS users was not affected and no data was lost.