They are taking on additional - and strictly speaking illegal - hours to "keep services going" and maintain patient safety, according to Bob Greatorex, council lead for workforce planning and professional standards.
This is despite almost all NHS trusts now claiming to be compliant with the European Working Time Directive (EWTD), which came into force in August 2009.
At the time 77 trusts in England were allowed to deviate from the directive, enabling doctors to work up to 52 hours a week.
Of those, 57 have just replied to Freedom of Information requests fromBritish Medical Journal Careers, claiming their rotas are now all compliant with the 48 hour limit. The other 20 did not reply.
But Mr Greatorex doubted this was the truth of the matter. He said many trainees worked on top of the 48 hour limit as "internal locums", hours not recorded under the system.
"They are doing this in order to keep services going and for patient safety purposes," he said, explaining that the 48-hour rotas often meant there were not enough doctors on duty.
He added that the directive was "still a significant issue that needs addressing".
Anecdotal evidence suggested it remained a problem for many specialities, he said, not just surgeons.