More than three-quarters of doctors say they are not confident the NHS will avoid failure in its new computer system, according to a BBC survey.
The scheme includes an electronic booking system
Only 7% of the 500 GPs and hospital doctors questioned for the Radio 4 File On 4 survey felt they had been adequately consulted.
The multi-billion-pound project will give each patient an electronic record.
The NHS head of IT said thousands of clinicians are involved but there was work to do in winning over doctors.
The 10-year IT programme includes plans to give 50 million patients in England an electronic health record.
Patients should also be able to book appointments and operations using an electronic booking system.
Dr Paul Cundy, chairman of the joint British Medical Association and Royal College of General Practitioners' IT committee, said it was "an accepted fact that the profession had not been properly consulted".
"We know from past disasters and investigations that if you want to implement things successfully in the NHS you must engage clinicians first," he told BBC News.
"To put it in easy terms, we have been banging on the door to say 'we have expertise that you could benefit from'."
Uncertainty about what the modernisation would mean had led to concerns among clinicians.
And plans for a national database was causing the joint committee concern about privacy and confidentiality, he said.
Richard Granger, Director General of IT for the NHS, said the programme recognised "the vital importance of engaging clinicians" but acknowledged there was "more work to do".
"Up and down the country every day, clinicians are involved in decisions about the national programme," he told BBC News Online.
"We're also strengthening the arrangements for clinical engagement, recruiting a team of senior GPs, hospital doctors, nurses and other health professionals to lead this work."
This week it was reported that the final cost of modernising NHS computer systems could rise to between £18.6bn and £31bn - three to five times the declared figure.
The inflated sum would eat into already overstretched trusts' budgets, the magazine Computer Weekly said.
But Health Minister John Hutton said the NHS would not be expected to carry an unsustainable financial burden.
File on 4 will be broadcast on Radio 4 on Tuesday 19 October at 2000 BST and repeated at 1700 BST on Sunday 24 October.