Cases of the deadly superbugs MRSA and C difficile must be reduced by 10% and 20% respectively by March 2009, the Health Minister said last night.
At the same time as setting the targets, Michael McGimpsey also launched Northern Ireland's first leaflet for patients and visitors on infection prevention which will be distributed to hospitals in the province.
In addition, Mr McGimpsey commissioned a second independent audit of environmental cleanliness standards in Northern Ireland's hospitals. The audit is to take place before the end of the year.
Announcing the targets, Mr McGimpsey said he is committed to combating the spread of hospital acquired infections.
"There has been substantial investment of £0.5m per year across the health service to ensure that the highest levels of hygiene and clinical excellence are maintained," he said.
"Important initiatives and strategies have been introduced to help reduce the rates of infection and improve cleanliness in our hospitals and since 2002 Trusts have been required to carry out mandatory surveillance of MRSA bacteraemias.
"Even though we already have the best infection prevalence figures for any part of the UK, we want these to reduce further."