And a third of trusts are not addressing skills gaps among directors of infection prevention and control, according to a report by the Healthcare Commission.
The study, Healthcare Associated Infection: what else can the NHS do? emphasises that while trust boards have to balance priorities, the safety of patients is paramount.
It found that 31 per cent of trusts were going against Department of Health guidance by failing to give directors of infection control personal development plans that addressed competency deficiencies.
Healthcare Commission safety strategy lead Murray Devine said: 'To be credible, a director of infection control would either need to be a master of their subject or have a skilled team around them.
'Not addressing possible competency deficiencies is a risk.'
The report, based on questionnaires, discovered that of directors of infection control who did have a related qualification, 45 per cent were microbiologists, infection control doctors or consultants in infectious diseases. Five per cent were infection control nurses.
Where the director was a doctor without a professional qualification in infection control, there tended to be a higher rate of MRSA.
The report also highlights the difficulty many trusts face in reconciling the management of healthcare-acquired infections and cleanliness with fulfilling other targets.
Financial targets were mentioned as a problem by 36 per cent of trusts and accident and emergency targets by nearly half.
Mr Devine said: 'People are trying to keep up with targets and that can result in compromises to safety.
'Wards have to be closed after an outbreak, but too often there haven't been the necessary conversations at board level or with strategic health authorities or Monitor.'
Trusts should review their self-assessments, which form part of the annual healthcheck, against the issues raised in the report, it says.
Extra measures should be considered, such as programmes to check bed cleaning, which 46 per cent of trusts surveyed do not currently have.