Widespread failings by NHS trusts will be exposed this week in the most comprehensive assessment yet of NHS performance.

The 570 hospital and primary care trusts in England are bracing for poor results from the annual health check - measuring the safety and quality of care - by the Healthcare Commission, the NHS watchdog, to be published on Thursday.

Medical organisations warned that a critical report on the state of the NHS could do more harm than good if it sapped morale and damaged patient care.

But officials at the commission countered that it would be pointless introducing a new measure intended to drive up standards if "everyone passed it".

Self assessments by the trusts have already shown many are failing to ensure that treatment provided to patients is safe, effective and well managed. Two thirds of trusts admitted they had failed to meet all the commission's 44 core standards including treating patients with dignity and respect, providing a choice of food and adequate training for staff.

A quarter of trusts said they had lapsed on at least four standards and 10 said they had missed at least 14, the commission's threshold for branding their performance "weak", in results published in July.

The ratings, which will include the self assessments, will rank trusts on quality of care and financial performance and replace the star rating system used in previous years.

Gary Needle, the head of the annual health check at the Healthcare Commission, said the new ratings to be published on Thursday would "feel tougher to trusts, particularly in the first year".

That alarmed medical organisations, which say poor results could further undermine the confidence of staff and patients at a time when the NHS is facing ward closures and cutbacks.

They are also likely to embarrass ministers who have insisted that the financial crisis in the NHS, which ended last year with a record deficit of £528m had not hurt patient care.

Patricia Hewitt, the Secretary of State for Health, conceded that the current reorganisation of the NHS, which has sparked protests, would lead to the closure of some accident and emergency departments. Asked on BBC1's The Politics Show whether there would eventually be a smaller number of hospitals with a full range of services, including A&E, she said: "Almost certainly."

The changes were a response to the changing nature of medicine, she said, adding: "What we will see, and what's already happening, is some hospitals will offer emergency surgery, others will only do the planned care, and that is much better."

Nigel Edwards, the policy director of the NHS Confederation, said: " If [the health check] adds to the general air of malaise, the Healthcare Commission may regret that. If you tell staff they are working for a crisis-ridden sinking ship, it may do more damage than the benefits gained from identifying areas for improvement. Because the health check is going to be more demanding [than star ratings] it may well look as if things have gone backwards, when it is clear they have gone forwards."

Jonathan Fielden, the chairman of the British Medical Association's consultants committee, said:"There should be a broader picture of how the NHS is working but it must be used to show how things can be improved, not as a stick to beat trusts with."

* David Cameron will set out plans today to give the NHS greater protection from political interference. The Conservative "independence Bill" for the NHS would put crucial decisions on its running and resources beyond the control of ministers by 2008.