Trusts are being unfairly marked down in their annual performance ratings because of changing targets and over-reliance on patient data, according to managers.

The complaints about the annual health check have come to light in Healthcare Commission board minutes. The minutes reveal concerns from the NHS Confederation over the consistency of the assessment across the service and the need to check that boards are engaged with the process.

In addition, the Foundation Trust Network said there were problems with targets, how scores are aggregated, and the involvement of patients in the process.

Network director Sue Slipman told HSJ that trusts were being expected to hit targets before they were mandatory. For example, last year they were judged on their ability to provide access to genito-urinary services within 48 hours even though the target did not come into force until 2008.

She said: "It makes trusts look as if they're offering bad services when in fact it isn't meant to apply to them yet. Most people were expecting an interim target."

Other targets, such as on MRSA infection rates, were calculated differently halfway through the year or had changed, she said.

Ms Slipman also criticised the extent to which patient survey results were used. "There's objective information such as patients' records we can use to establish facts," she said.

The minutes also reveal that a survey of 220 trusts' views on the 2006-07 annual health check had found "frustration" over duplication with other regulators, concerns and confusion about follow-up inspections and concern about the comparability of scores across trusts. However, 93 per cent of trusts thought it had a positive impact on care.

A Healthcare Commission spokesman said concerns were being addressed at the "highest levels" of the organisation.

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