Doctors in certain areas will be able to work longer hours than others
The government has said not all doctors will have their working week cut to 48 hours in August as planned.
Ministers have opted out from the European Working Time Directive, meaning the limit will not go down to 48 hours for another two years.
Instead, they will remain able to work up to 52-hours a week.
Doctors' associations, which had said the shorter week did not allow enough training time, welcomed the move, but said it did not go far enough.
The opt-out means that junior doctors will be able to work four extra hours if their employer chooses.
The move is now being considered by the European Union, which will give its opinion in three months' time.
All UK employees working more than 48 hours a week can voluntarily opt out of the hours rules of the European Working Time Directive (EWTD) and work up to 78 hours per week.
This is as long as they do not more than a 13-hour shift with one day off every week or two days a fortnight.
Two-thirds of doctors in the UK already work a 48-hour week.
The Royal College of Surgeons has warned staff levels are being cut too much and there is less overlap between doctors' shifts, so handovers are more rushed - and unsafe.
However, a small study published this week found that doctors who did work fewer hours did not make as many medical errors.
The government said there were other "specific and unavoidable" reasons why some could not meet that target, including a shortage of doctors and split-site services, which require more doctors than normal.
The opt-out, or "derogation", is expected to last for up to three years.
It will apply to doctors in training who have duties in services that are delivering 24-hour immediate patient care, in some extremely specialist areas or in small, remote or rural units.
But the government said it was committed to all doctors working within the 48-hour week.
Health Minister Ann Keen said: "Most UK doctors in training already comply with the EWTD, and the overwhelming majority will do so by 1 August this year.
"However, we have notified the European Commission that we intend to operate a derogation for a small number of services involved in delivering urgent and emergency patient care.
"For unavoidable and specific reasons, this small number of services is unlikely to be able to fully implement the EWTD by 1 August, 2009.
"Potential reasons include services in trusts which are relatively isolated from large population centres and so find it difficult to recruit more doctors, or where hospital services are in the midst of change programmes."
But a spokesman for the Royal College of Surgeons said: "Surgeons are clear that an impending crisis in quality patient care can only be headed off by working 65 hours a week, including on call.
"The Department of Health announcement will do little to ease concerns.
"We will continue to campaign for a surgical specialty opt out for both surgeons and surgical trainees to protect patient care and ensure highest standards in training can be maintained."
Professor Ian Gilmore, president of the Royal College of Physicians added: "While derogation provides for only an additional four hours, this will undoubtedly afford some vitally needed breathing space for some services while the profession, with government develops a more sustainable solution to the acute challenge the service now faces in providing quality clinical care."