More than a quarter of NHS trusts in England are at risk of losing their licence to treat patients because of a failure to comply with hygiene regulations, the government's health watchdog said on Monday.

The Healthcare Commission said 41 hospitals and 62 other NHS organisations had admitted failing to observe one or more core parts of the hygiene code, introduced in 2006 amid concern about the spread of MRSA, Clostridium difficile and other hospital "superbugs".

The figures represent a slight increase in the number of trusts admitting non-compliance over the past year, despite a deep-clean programme ordered by Prime Minister Gordon Brown and repeated warnings by the Department of Health.

Anna Walker, the commission's chief executive, said the trusts had 10 months to clean up their act before a tougher regulatory regime is introduced in April.

NHS trusts will have to pass a hygiene test before they can be registered by a new care quality commission.

"The picture on hospital-acquired infection is mixed," Walker said. "There were improvements in two out of the three relevant standards. But overall we are still in a situation where too many trusts have self-declared non-compliant."

The most common problem was a failure to keep up with a recent toughening of guidelines on equipment decontamination.

The Healthcare Commission data is based on information provided by 391 trusts in England. Details of how all organisations declared can be found here