More than one in eight hospitals have under-reported the number of MRSA infections for as long as three and a half years, new documents reveal.

Fears about the true scale of the superbug problems in Britain's hospitals grew today as the Department of Health admitted for the first time that 13 per cent of trusts had broken their own rules on reporting cases. They had excluded from official reports cases of MRSA infection in patients believed to have had the bug before coming into hospital.

Since April 2001, all trusts have been required to report all MRSA bloodstream infections, regardless of where patients acquired it.

But an unpublished survey carried out by the DoH last year revealed that some trusts had failed to comply with this, resulting in an inaccurate picture of the scale of the problem in trusts.

The Nursing Times will report this week that the Department of Health discovered the under-reporting, and then gave the trusts a chance to amend their figures. The latest national MRSA data published in March, covering the last six months of 2004, now reflects all cases.

But the scale of the under-reporting means that some hospitals would have looked much better than others on the official statistics, and may not have instituted the right infection controls as quickly as necessary. It also means the public was given a false picture of the state of superbug infections in some hospitals.

England's chief nursing officer, Chris Beasley, and the chief medical officer, Sir Liam Donaldson, have now written to trusts ordering them to submit accurate data.

A DoH spokesperson told Nursing Times that the problems had now been cleared up. 'This has had little impact on overall figures. If anything, this would make it more challenging for trusts to achieve the 50 per cent reduction in rates by 2008.'

Infection control in hospitals is becoming a major issue for the government as other superbugs appear to be as big a problem as MRSA, although the scale of them is only just emerging.

Health Secretary Patricia Hewitt announced last week that she would order an inquiry into an outbreak of a virulent new strain of the bug Clostridium difficile at Stoke Mandeville hospital, where it has claimed 12 lives and infected 300 people since the end of 2003. Nationally, C. difficile is killing twice as many people as MRSA.