Patients are to have a greater say in deciding which medical doctors receive bonus payments, the government announced this week.
But the Council of Heads of Medical Schools is cautioning that the awards should still be made to clinical academics and that universities should continue to be represented on the awards body.
About 3,300 consultants hold a merit award, each of which is worth Pounds 23,000 to Pounds 55,000 a year. With a merit award, consultants earning the top salary of Pounds 57,800 can take their National Health Service income above Pounds 112,000 a year.
"It is very, very important that clinical academic staff have the same opportunities as others to receive a merit award," said Michael Powell of the CHMS. "If the opportunity is diminished, there will be a risk of clinical academic careers becoming less attractive, and that would, in turn, risk the long-term future of the NHS."
The body that makes the awards, the Advisory Committee on Distinction Awards, is to be slimmed down from 33 to 14 members, the government said. At present, 25 consultants sit on the committee; this will be cut to five. The other eight members will be representatives of NHS employer and patient interests.
Mr Powell pointed to the role of the universities on the awards panel. "I believe it is very important that universities continue to be represented on the committee," he said. "It is very important that the high quality of academic medicine is maintained."
The reforms were announced after concerns that the system had become an old boys' network. One of the surgeons who was struck off the medical register following the deaths of 29 infants and children at the Bristol Royal Infirmary is still benefiting from his bonus.
There are also concerns that the allocation of merit awards is racist and sexist. A white doctor is three times as likely to receive an award as an ethnic minority colleague, and a male doctor is twice as likely to receive an award as a female colleague, according to Sam Everington, a member of the British Medical Association's council.