Managers at Oxford's largest hospitals are frustrated by NHS ratings revealed today which they claim overshadow their hard work over the past year.

The Oxford Radcliffe Hospitals NHS Trust appealed to the Healthcare Commission to reconsider its final results after receiving a "weak" financial ranking.

Even though the trust - which oversees Oxford's John Radcliffe and Churchill Hospitals, and The Horton in Banbury - was assessed as "good" for four out of the five financial factors, it was still awarded the lowest rating for finishing 2006/7 in deficit.

The Nuffield Orthopaedic Centre blamed computer software for patient waiting time breaches.

Despite asking the commission to consider the problem as "extenuating circumstances", it led to a "weak" rating for the quality of its services.

It is the second year the Healthcare Commission has used the current NHS rating system, which replaced the former star rating for the UK's 394 trusts.

Trusts are marked for both the quality of their services and their finances, known as use of resources.

The ORH's quality of services dropped in standard from good last year to fair, due to problems such as too many patients infected with MRSA, and the hospitals' failure to give people privacy and dignity.

A spokesman added that the weak score for use of resources failed to take into account that although it ended the year in the red, it was less than the planned £9m deficit.

She said: "The trust appealed to the Audit Commission about this anomaly and, although there was sympathy for the trust's position, it ruled no exemption could be made to the standard methodology."

Chief executive Trevor Campbell Davis thanked staff for their work and added: "Last year was a very busy one for the trust. We reduced our costs by £34m. We also met all the main targets and substantially cut waiting times for patients.

"We'd all have been delighted if we'd improved our ratings in the annual health check at the same time, and it's frustrating for staff that we so narrowly missed out."

NOC managers blamed a new NHS computer system for preventing 30 patients being treated within 26 weeks, and for wrongly reporting that urgent cancer patients were not seen within two weeks.

Chief executive Jan Fowler said: "The Healthcare Commission's overall ratings don't reflect the high quality service we're delivering at the NOC.

"We'd hoped the Healthcare Commission would accept there were extenuating circumstances in respect of the issues around our waiting time breaches."

Healthcare Commission south central area manager Kate Godfrey said the ORH's appeal had been dealt with by the Audit Commission, and the Healthcare Commission just published their results.

She added: "As far as the NOC's concerned the IT problem was a recurring issue for them two years in a row.

"We understand their frustration, but the bottom line is some patients weren't seen in time."