A loss of medical professionalism will lead more doctors to quit the career entirely, according to trainee medics.
Some felt there was too much emphasis on form filling
A poll of more than 2,000 future doctors found eight out of 10 shared this concern.
They said factors outside medicine, such as public expectations, may undermine a good relationship between doctor and patient.
The Royal College of Physicians' survey was carried out with the help of the British Medical Association.
Other factors judged as having a detrimental effect on medical professionalism included the expectations of policy makers set in the context of limited financial resources.
Changes in working patterns and medical education, as well as protocol-driven care were also blamed.
The trainees said that over the past five years there had been an increase in clinicians' responsibilities but a concurrent decrease in their autonomy.
Rather than being able to make independent choices based on clinical judgement, many felt that decisions had to be based on issues surrounding money and targets.
Others said the introduction of the European Working Time Directive was affecting continuity of care and leading to a culture of doctors who "clock on and clock off".
Dr Declan Chard, chair of the RCP's trainees committee, said: "Junior doctors and medical students believe that professionalism is not optional but an essential part of being a doctor - it is at the core of our relationship with patients.
"Sadly many trainees believe that medical professionalism is being challenged to a degree that they may consider leaving medicine.
"Ultimately this will have a negative effect on patient care.
"If the NHS hopes to retain its doctors and fully support them in their work, it should more overtly value medical professionalism."
A Department of Health spokeswoman said: "The new junior doctors training programme Modernising Medical Careers (MMC) is designed to raise the standards of training and improve the relationship between doctor and patient so that patients receive high quality care from skilled, professional, empathic doctors.
"The BMA and all relevant Royal Colleges were heavily involved in deciding the curriculum programme for MMC."
She said patient safety and care was always top priority adding: "Although European Working Time Directive compliance is a local matter, we gave support through the Hospital at Night pilots which included good practice on shift and role design"..
She said NHS funding had also improved and that targets were helping patients to get treatment faster.
Dr Chard said: "While MMC usefully addresses many training issues, it has not necessarily looked at the professional values that underpin medical practice."
"Also, trainees have a number of concerns about shift working patterns, introduced as a result of the EWTD. While shorter working hours allow doctors to be more refreshed and ready to work, patient care and training appears to be more fragmented."
He said that continuity of care may have been compromised. "Through continuity of care, junior doctors gain valuable educational feedback, and I believe this encourages commitment to individual patients from admission to discharge."
The survey results come ahead of a report on medical professionalism due to be published by the RCP next week.