There have been concerns the limited hours would affect training
European rules preventing trainee doctors from working more than 48 hours a week have come into force.
Doctors' organisations have criticised the European Working Time Directive, saying the reduced hours means there is too little time to provide training.
And there have been concerns it could hamper the NHS response to swine flu.
But the government says 97% of the NHS has already met the new requirements, with no effect on training, and plans are in place to cope with swine flu.
In the mid-1990s, some junior doctors had working weeks which typically topped 100 hours.
The directive took effect for many other workers in 1998, but the changes to reduce doctors' working hours were incremental and began with consultants.
Royal College of Surgeons President John Black's concerns
By 2004, junior doctors were included in a 58-hour working week target and by 2007 this was down to a 56-hour week.
As of 1 August, the target will be 48-hour-weeks for the UK's 60,000 junior doctors.
Contracts asking trainee doctors to work outside the regulations will be illegal and all rotas must be based on the 48-hour model.
But individual doctors can opt out, although this has to be voluntary.
However doctors cannot opt out of taking 11 hours continuous rest out of 24, or out of ensuring they have 24 hours continuous rest out of each seven days.
A spokesman for the Department of Health said: "Where a service needs additional hours of cover individual doctors can voluntarily opt-out of the 48-hour limit to provide this."
The quality of training is under review
Only a few specialist areas will be exempt from the new rules.
But the British Medical Association said evidence on the ground contradicted the claim that the NHS was ready for the change.
Dr Andy Thornley, chairman of the BMA's junior doctors committee, said: "We are not reassured by government reports that the NHS is 97% compliant with the new working time regulation as we fear many junior doctors are being pressured to lie about their hours.
"And our members are worried about their training; many feel it has reduced in quality as working hours have been reduced."
He said it was possible to meet training demands and maintain patient services, but that managers would need to rely more on consultants than they do now.
Max Pemberton, a junior NHS doctor working in mental health, said things were easier since he stopped working 48-hours a week, but added many of his friends in surgery still worked more than 56.
NHS organisations have told us consistently that they are ready
David Grantham, NHS Employers
He told the BBC's Today programme: "The issue is junior doctors don't want to work excessive hours because it's not safe for patients. The concern is they still need to get the training in.
"Since 2007 there has been quite a dramatic reduction in the amount of years it takes to get from being a junior doctor to a consultant.
"So the government has concertinaed all of those usual years into just a few years and now we're seeing a further reduction in hours of actual working."
Dr Sheree Datta, a junior doctor at Brighton's Royal Sussex County Hospital, told the BBC: "The reality is when you're running a short staffed unit it can be very difficult to make sure you've got enough staff on the shop floor."
John Black, president of the Royal College of Surgeons, said the government had failed to listen to its concerns about needs within surgery.
"It is sophistry for the Department of Health to on the one hand deny an opt-out for surgeons that would enable us to organise safe patient care and good training but then hope doctors will opt-out individually to cover staff shortages to keep the service running."
But David Grantham, of NHS Employers, said: "NHS organisations have told us consistently that they are ready for implementation of the directive for junior doctors.
He added: "It remains appropriate that outside of exceptional or emergency circumstances, such as a flu pandemic, doctors like other health professionals, and their patients, should be protected by the reasonable controls on working hours set out in the working time regulations."
A Department of Health spokesman said there was no evidence training had become less effective.
"The quality of training and supervision is more important than the quantity of hours completed," he said.
"We know that junior doctors are concerned about their training and that is why the Secretary of State has asked Medical Education England to review the quality of training in the light of the directive to see if any adjustments need to be made."
This page is best viewed in an up-to-date web browser with style sheets (CSS) enabled. While you will be able to view the content of this page in your current browser, you will not be able to get the full visual experience. Please consider upgrading your browser software or enabling style sheets (CSS) if you are able to do so.