NHS trusts have been served with a 'wake-up call' to improve hygiene standards or risk service closures, following the latest annual health check declarations.
More than a quarter of trusts have told the Healthcare Commission they failed to comply fully with the hygiene code in 2007-08.
From as early as next April, all acute trusts, and possibly other sectors, will have to comply with the code to register with the new regulator, the Care Quality Commission.
If they do not register, trusts will not be licensed to treat patients.
But 24 per cent of acute trusts and 37 per cent of primary care trusts said they were not meeting all the standards included in the code.
The real figure could be even higher, the Healthcare Commission warned.
Compared with last year, compliance has worsened in three areas: acting on safety notices, use of medical devices and decontamination of medical equipment.
Healthcare Commission chief executive Anna Walker said: "It's incredibly important both for patients and the trusts themselves that these standards are met.
"This is a wake-up call 10 months before formal registration."
Ms Walker said she hopes most struggling trusts will be able to register with conditions attached, rather than close.
Registration for standards unrelated to hygiene will be introduced in April 2010. The government is currently consulting on what these registration requirements should contain.
The Healthcare Commission will now carry out risk-based and random inspections to check whether trusts' self-assessments are accurate, before publishing their findings in October.
Overall, 96 per cent of trusts say they have complied with core standards making up the annual health check, compared with 94 per cent in 2006-07.