Rotas at 77 hospital trusts in England were "derogated" from the EWTD when it was introduced in August 2009, allowing them to operate at a maximum of 52 hours a week instead of 48 hours until 31 July 2011.
A total of 57 trusts that responded to a freedom of information request by BMJ Careers
confirmed that their training rotas are now compliant with the 48 hour limit stipulated in the directive.
Some trusts had made their derogated rotas compliant with the 48 hour limit as of 2009, whereas others, such as Peterborough and Stamford Hospitals Trust, had only ensured compliance by October this year.
Alder Hey Children's NHS Foundation Trust reported difficulty recruiting for some posts, but said it expects the rotas to be compliant this autumn.
Ben Molyneux, deputy chair of the BMA's Junior Doctors Committee welcomed the news. "I would be very concerned if they hadn't done it," he said. "If they are operating outside of 48 hours they're operating illegally."