Health inspectors demanded urgent action last night to remedy failings at 50 NHS trusts across England that scored the worst marks in a new tougher system of measuring the quality of patient care. The Healthcare Commission confirmed a report in the Guardian yesterday that it has graded nearly half the country's hospitals and other healthcare organisations as "weak" in the NHS's first annual health check published today.

It placed 236 of the 570 trusts in the lowest category, rating some as weak for poor stewardship of resources and others for inadequate control of the quality of patient care. Eight hospitals, four ambulance services, one mental health trust and 11 primary care trusts (PCTs) achieved the unenviable distinction of being weak on both counts.

Anna Walker, the commission's chief executive, said urgent steps were needed to improve performance in 50 trusts with the lowest quality of patient care. Their defects included failure to ensure proper decontamination of medical equipment, lack of staff training and poor management of patient records.

She said strategic health authorities would ask the trusts to produce action plans within 30 days on how to come up to minimum standards. They would also look into the performance of 290 trusts whose quality was deemed to be no better than "fair".

Ms Walker said: "Poorer performance is in areas that really matter to patients. A significant number of PCTs are failing to provide out-of-hours crisis care. MRSA [the hospital superbug] targets still need vigorous action. And trusts report not meeting standards on compulsory training and use of medical equipment."

Sir Ian Kennedy, the commission chairman, said the new system was largely based on trusts owning up to poor performance, although the commission ran checks to ensure honesty. About 43% of trusts should be praised for admitting shortcomings and starting on "a journey of improvement".

He added: "Patients will want the NHS to raise its game still further. They need a universal guarantee that trusts are meeting general standards ... We expect these standards will be met next year."

The report gave top marks to only two trusts, both foundation hospitals with independence from Whitehall control.

Harrogate and the Royal Marsden, a specialist cancer hospital in London, got an "excellent/excellent" rating in recognition of their high performance on finance and quality.

Sue Slipman, director of the foundation trust network, said the results showed its members were "way ahead of the game", with 87% graded as good or excellent on use of resources. However, Moorfields foundation hospital, the country's premier ophthalmic centre, was ranked as weak on quality of care.

Among all types of trusts, 36% scored good on quality of services and 4% were excellent. Just 12% were found to be good at managing their finances and 3% were excellent.

Sources at the Department of Health said the commission may have been unduly harsh in its interpretation of financial data provided by the Audit Commission. It was understood that ministers asked the commission to explain why the scores of 50 PCTs were improved a few hours before publication. Without this late adjustment, more than 30 trusts would have got a weak/weak rating.

But in public, Patricia Hewitt, the health secretary, supported the commission for "the toughest and most comprehensive assessment of the NHS ever made". She said: "There is no doubt the NHS has made big improvements ... but, as these results show, there needs to be more improvement. I can reassure patients that staff in all NHS hospitals will continue to give good, safe care."

Andrew Lansley, the Tory health spokesman, said: "It is a pretty sorry state of affairs when nine out of 10 PCTs have been rated only weak or fair. Even with an increase in resources, the government's policy of using PCTs to manage NHS resources is failing. The healthcheck is at least a dramatic improvement on the discredited star ratings used by ministers over previous years. These results serve to show the weakness of the management by ministers themselves."

Niall Dickson, chief executive of the King's Fund health research institute, questioned the reliability of trusts' self-assessments. "We are concerned that many across the country overestimated their levels and had their standards revised by the commission," he said.

Gordon Lishman, director general of Age Concern England, said: "The performance assessment ratings largely bypass patients' views and are the equivalent of asking students to mark their own exam papers."

· Scores for every NHS trust at Healthcarecommission.org.uk/annualhealthcheckratings