Some NHS trusts have warned they face staff shortages in specialist areas as they try to meet a new limit on junior doctors' hours coming into force.
Trainee doctors will see their working patterns change
Trainee doctors should no longer be working more than 58 hours a week under European regulations.
Some trusts have recruited more doctors and extended nurses' roles, but polls suggest around 16% cannot comply yet.
Doctors' leaders say they will back any medic working over the limit who wants to take legal action.
The hours limit is enshrined in the European Working Time Directive.
The directive, introduced in 1998, limited most workers' weeks to a maximum of 48 hours.
But it was agreed that junior doctors could be excluded from the ruling because of the difficulties of cutting their hours to meet that limit. In the 1990s, doctors could be working 80-hour weeks.
Sunday's introduction of a 58-hour limit is the first stage of reducing junior doctors' hours to match everyone else's. Trusts face fines of up to £5,000 if they do not comply.
By August 2007, they should be working 56-hour weeks, and by August 2009, 48 hours.
One junior doctor, David Macklin, told the BBC the reduction was crucial for patient safety and doctor's working lives.
"You wouldn't want to be in a plane flown by a pilot who hadn't slept for two days. Why would you want to be looked after by a doctor who hadn't slept for a similar period?" he said.
NHS trusts have found it difficult to meet this first working time directive deadline because it involves a major shift in how doctors' work is organised.
They say there are problems in some areas such as paediatrics and maternity services, there is a shortage of doctors, and some hospitals are finding it difficult to introduce the new system.
Reductions have not taken into account 'on-call' time, where a doctor is at the hospital, but may be asleep.
But a European Court of Justice ruling said under the Working Time Directive, it should be taken into account - so trusts have had to bring in shift working to ensure enough doctors are available.
A second ruling said doctors had to be compensated for rest time lost before they started their next shift.
Dr Simon Eccles, chairman of the BMA's junior doctors committee, said the regulations were being introduced to protect patients as well as doctors.
But the BMA fears the shift systems could harm doctors' training, as those working nights are likely to witness fewer procedures to learn from than those working days.
Dr Eccles added: "Junior doctors are in hospitals to learn as well as look after patients. Safe hours must not mean unsafe training."
Chris Atkinson of the NHS Confederation, which represents hospital trusts, said most hospitals had met requirements but staff were short in some specialities.
He added: "Patients will benefit because doctors will be working fewer hours and will be less tired so standards of care should be increased."
Shadow health secretary Andrew Lansley said the new rules caused smaller hospitals serious problems in maintaining services and damage was being done to the NHS.
He blamed the government for signing up to the Working Time Directive and said: "The combination of EU regulation and government incompetence is doing real damage to the NHS."