Hospitals are being tempted to employ "dangerous working practices" to meet European rules on doctors' hours, the body representing surgeons alleges.
The Royal College of Surgeons says data shows the number of rotas reportedly complying with the 48-hour week fell from 78% in March to 72% in April.
There are 3,000 doctor posts currently vacant in the UK, the college says.
But, it warns, there are not enough medics to fill these posts under the current working restrictions.
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.
But by 1 August this year, all trusts are meant to comply with the regulations. Last week, the government said it would review how the EU working time directive will impact on junior doctors amid concerns that it could harm the quality of their training.
The College said it expected the number of rotas which complied with the working time directive to fall even further as the August deadline approaches.
"Moving to 48 hour working with current staffing means losing half a million hours of doctor-patient time a year from the NHS and the NHS is struggling to cope," said its president John Black.
"You only have to look at the recent Healthcare Commission report into the failing Mid-Staffordshire NHS Trust, which found that low staffed surgical rotas was one of the main contributing factors to the breakdown in patient care."
A spokesman for the Department of Health said: "Strategic Health Authorities have worked with the Royal College liaison teams to provide expert advice and support to those services who may require additional support beyond the August 1 deadline.
"In January we notified the European Commission of our intention to derogate which will mean a working week up to 52 hours up to 2011 and exceptionally to 2012 for a small number of 24-hour immediate patient care services."
David Grantham of NHS Employers said: "The NHS has been working hard to implement the EWTD, with the support of other stakeholders, including the British Medical Association.
"There are challenges but there is good progress. Where there are problems arrangements are in place to maintain services and standards during transition."