A quarter of hospital trusts in England are failing to meet new standards on infection control, a survey by the Healthcare Commission has found.
Forty-four trusts were not complying with one or all aspects of the hygiene code, standards seen as key after the recent deaths from hospital infections.
The general picture in the watchdog's annual health check of England's trusts was, however, one of improvement.
But regional divides persist, with the north performing better than the south.
Trusts were rated on two principle categories: quality of services and how they had managed their finances.
NHS RATINGS 2007
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Nineteen trusts scored "excellent" on both parts of the rating, up from two last year.
But 20 were deemed "weak" - the lowest scoring - on both counts, four of these for two years in a row.
Health Secretary Alan Johnson said he had asked the commission to re-inspect the 44 trusts failing on infection.
He also said that if the chief executive of the NHS was unable to resolve the situation through talks with the boards at the four weakest hospitals, one option would be a takeover by a well performing trust.
The four comprise West Hertfordshire Hospitals NHS Trust, Surrey and Sussex Healthcare Trust, Northern Devon Healthcare Trust and Royal Cornwall Hospitals NHS Trust.
Health Minister Ben Bradshaw told BBC Breakfast that the situation was "not acceptable" but that progress was being made.
He added: "Just because these trusts do not meet one of these codes does not mean that their treatment or the hospitals are unsafe, or that patients need to worry about them."
Every trust achieved the target for cancer patients waiting no more than a month between diagnosis and treatment, except for sound clinical reasons.
Despite increases in patient numbers, A&E waiting times were met nationally, with 98% of 18 million patients receiving care within four hours.
Meanwhile, the proportion of operations which were cancelled fell for the third year in a row.
But there were targets not being met: some 70% were failing on "convenience and choice", which says patients should be able to choose from four different NHS providers.
This, the commission said, was primarily because GPs were not contractually obliged to offer the choice, and technical problems with the computer booking system were not uncommon.
The disappointing findings on infection control were partially mitigated by the fact that new and more rigorous standards were introduced in October 2006, the commission said.
"The bar was raised dramatically on infection control and that explains why trusts seem to be performing worse than in the past," said chief executive Anna Walker.
But the findings on the failure of some trusts to ensure hygiene standards - including cleaning hands and instruments - comes just a week after serious such shortcomings at the Maidstone and Tunbridge Wells NHS Trust were blamed for the deaths of up to 90 patients from C. difficile.
North and South
The trust was one of the 20 which scored poorly in both categories, the majority of which were found in the south of the country.
Overall, the South West strategic health authority (SHA), one of the 10 covering the country, had the highest proportion of weak trusts. The South East Coast SHA had the lowest proportion of "excellent" trusts and the highest combination of "weak" and "fair".
Basingstoke and North Hampshire
Birmingham Children's Hospital
Calderdale and Huddersfield
Cambridge University Hospitals
Chelsea and Westminster Hospital
Chesterfield Royal Hospital
Frimley Park Hospital
Guy's and St Thomas', London
Heart of England
Liverpool Women's Hospital
Queen Victoria Hospital
Sheffield Teaching Hospitals
Yeovil District Hospital
South Essex Partnership
South Staffordshire Healthcare
Trusts rated excellent in both principle categories
The East Midlands SHA had the highest proportion of "excellent" trusts and the North East SHA had the highest combination of "excellent" and "good" trusts.
The commission said the division was a long-standing one which was only starting to come to light as a result of the surveys it carried out.
"There has been historic poor performance in these areas, but it's only now there's been a spotlight on them," said Ms Walker.
"Hopefully now that it's out in the open improvements will be made, and trusts in the south can look at what they can learn from the north."
Health Secretary Alan Johnson said: "This independent verdict on the NHS shows clear improvement.
"The well-performing and improving trusts are to be congratulated, but we need to see more improvement from those classed as weak."
Dr Hamish Meldrum, British Medical Association chairman, welcomed the general improvement.
But he said: "We remain concerned that a number of trusts are continuing to under-perform.
"This is very disappointing news and it is vital, for the sake of patients, that these under-performance issues are urgently addressed."