Proposals to allow greater training flexibility must not pressure junior doctors to opt out of working-time rules, the BMA warns.
It warned opting out of EWTD must not be the result of changes to working-time regulations suggested by an independent review, and approved by the government.
The review, chaired by former Royal College of Surgeons of England president Norman Williams, suggests encouraging more widespread use of individual doctors' rights to opt out of the maximum 48-hour working week, where it was safe to do so.
It also recommends giving doctors more opportunities to train outside the 48-hour week and ensuring NHS trusts review working patterns and rotas to give doctors more access to training.
Working-time regulations mean doctors must not work longer than a maximum of 48 hours a week when averaged out across a six-month period.
However, the regulations have caused concern among some doctors, particularly those in surgical training, about the impact on their training time.
"We have to remember that the work and training of junior doctors are inseparable. This leads to unique pressures that can't be resolved just by increasing working hours," said BMA council chair Dr Mark Porter.
"Having the right degree of flexibility in the system is important, but we must not create a culture in which doctors feel pressured into opting out of the 48-hour weekly limit that protects patients."