Potentially infectious patients with MRSA were not isolated for up to 17 days because of difficulties with the Care Records Service - a central part of the NHS's £12.4bn National Programme for IT (NPfIT).
Details of the problems at Buckinghamshire Hospitals NHS Trust have emerged days after prime minister Gordon Brown promised "deep clean" measures to stop the spread of hospital infections.
Buckinghamshire went live in September 2006 with one of the first roll outs in the South of England of the Care Records Service, supplied by Fujitsu and Cerner. The trust had support from NHS Connecting for Health.
The government wants a care records service rolled out across the NHS in England to provide reliable medical records on 50 million people that can be accessed wherever a patient is being treated.
But in the 12 months after going live, Buckinghamshire has reported a series of problems, including difficulties collecting accurate data, which was "an area of major concern".
The trust reported that between March and July this year potentially infectious patients with MRSA were not isolated for between two and 17 days, because of what the trust said were problems with the Care Records Service.
A trust spokesman said last week, "The trust continues to work with Fujitsu to explore ways of resolving outstanding problems, including difficulties in tracking MRSA patients electronically, and the system will not be fully rolled out across the trust until these issues have been ironed out."
The spokesman said that hospitals do not rely solely on computer-based patient records systems for tracking patients with infections, and that alerts are included in patient notes.
However, trust board papers show that some patients were not isolated as staff were unaware they had MRSA because their medical records were "unavailable". In another case, notes were not marked.
The trust found that after going live at hospitals in Wycome and Amersham, staff needed to enter historical MRSA alerts on systems manually.
A trust board paper said, "This took approximately six weeks to do, during which time there was a possibility that some MRSA-positive patients may have slipped through undetected if medical notes had not been available.
"There have been several other problems with the system which have resulted in a small number of patients not being isolated promptly."
A trust spokesman said there had been no Care Records Service-related MRSA incidents since June.