Doctors often work very long hours
Surgery teams in many NHS hospitals are not ready for a likely fall next year in the maximum hours they are allowed to work, says a survey.
Failure to plan for the changes could hit patient safety and training, said the Royal Colleges representing surgeons and anaesthetists.
Under half of trusts who responded said they were hitting the 48-hour EU limit.
In theory, the UK currently has an opt-out, which allows some doctors to work longer - but that is under threat.
MEPs will debate a challenge to the opt-out next month.
The European Working Time Directive has proved a massive challenge for the NHS since it was first introduced in 1998, with many junior doctors working far in excess of 48 hours a week.
At first, junior staff were exempted from the directive, but a 58-hour limit was introduced in 2004, falling to 56 in August 2007, with the final drop to 48 by August 2009.
The UK, however, still has an opt-out, which allows doctors to sign away their right to a 48-hour week if they choose.
But specialists say that in practical terms, it would be extremely difficult to organise hospital rotas in which some doctors exercised this right and some did not.
In addition, European Parliament could decide to remove the the ability to opt-out, with the issue under debate next month, and the Department of Health has told trusts that they need to comply with the 48-hour limit.
The survey, from the Royal College of Surgeons and the Royal College of Anaesthetists, suggested that many hospitals are running out of time to make the changes needed to reach 48 hours.
Fewer than half of the surgical and anaesthetic work rotas provided by 66 trusts who responded complied with the limits.
Only 18% of trusts said their surgery staff were meeting the target, and only a third said this for their anaesthetic staff.
Those who said they were ready said it had taken them between six and 12 months to make the necessary changes.
John Black, the president of the Royal College of Surgeons, warned that the rush to meet the target could leave potentially dangerous staffing practices.
He called for more funding to help hospitals make the change.
"With the deadline looming, surgeons and anaesthetists are worried that NHS trusts will be tempted to simply cobble together rotas that fit the law but don't take proper account of night-time staff, ensure patients have as few handovers as possible or provide junior doctors with the varied training needed."
"Getting working hours down while offering proper, safe patient care and retaining medical training is not straightforward and takes time."
Dr Andy Thornley, chairman of the BMA's Junior Doctor Committee said there was still an opportunity for trusts to prepare ahead of the deadline.
"Trusts need to ensure junior doctors' rotas are well planned so that hospitals operate smoothly under the new working hours limit.
"There is still time for hospitals to address the challenges of junior doctors moving to a 48 hour week, but it is important that the change is carefully managed so that patient services are not disrupted and the quality of junior doctor training is not put in jeopardy."
A spokesman for the Department of Health said that it had been running pilot projects to help trusts move smoothly towards the 48-hour limit.
She said: "It is important that trusts learn from best practice in other parts of the NHS, including examples in this report and from NHS North West where 97% of doctors in training are already compliant with the 2009 - 48-hour week - requirements."
David Grantham, Head of Programmes at NHS Employers, said: "NHS organisations are working hard to ensure that junior doctors work no more that 48 hours per week from August 2009.
"The challenge is for clinicians and managers to work together to re-design services that deliver improved patient care and quality within the hours available, given that this is health and safety legislation.
"This will require new roles and ways of working. We expect to see the number of doctors working compliant patterns to increase as the deadline approaches and employers are aware that this is an important issue."
But Liberal Democrat health spokesman Norman Lamb said: "This is a ticking time bomb. Its essential we get a thorough assessment to see what the scale of this problem really is.
"Ministers must bring forward plans to ensure that we don't end up in a crisis next August."