The UK's National Health Service (NHS) had a shortage of 3,000 junior doctors at the end of 2008, the British Medical Association (BMA) said.
BMA said the problem was made worse because of inadequate preparations prior to the implementation of the 48-hour working week policy.
BMA Junior Doctors Committee leader Shree Datta said the problem of understaffed rotas has worsened because the government has mishandled changes to the immigration system, leading to many overseas doctors, who used to fill the staffing shortfall, leaving the UK.
"Doctors working on understaffed rotas have serious concerns about standards of patient care. For too long the NHS has relied on junior doctors working beyond their contracted hours, the time has come to stop papering over the cracks and deal with the issue," Datta said.
Datta said that greater use of non-resident doctors to work on-call in addition to reducing unnecessary bureaucracy could help junior doctors offer higher standards of patient care.