Health New Zealand has stepped up precautions after new break-outs of the infection known as antibiotic-resistant enterococci or VRE. Two different strains of VRE had been identified on one ward.
Health New Zealand said there were fewer than 10 patients with the infection, but many were asymptomatic carriers.
The bacteria is difficult to treat due to its antibiotic-resistance, and in some cases can be potentially life threatening.
VRE can spread within healthcare settings through surfaces, patient equipment and from a person's hands that have not been properly cleaned.
Health New Zealand's website said there had been an increase in the hospital patients colonised with VRE in some regions.
It was advising that all patients who stayed overnight at Waikato, Thames, Tauranga or Lakes Hospital, or been day patients in their renal or oncology wards, be screened and isolated while awaiting results.
Infectious diseases researcher at the University of Auckland, associate professor Mark Thomas, told Checkpoint VRE was a bacteria that lived in the intestines.
He said 90% of people didn't have a problem, however, the bacteria targeted people who were sick or vulnerable.
"About one in 10 people become sick," he said.
"[Health New Zealand] are trying to prevent the organism spreading widely in New Zealand, the fact is, it's very very hard once it's establish in a hospital to get rid of it.
"It's been in Waikato and Bay of Plenty hospitals for some years now, and I don't know that they are getting rid of it."
There was an opportunity to get rid of the bug when numbers were low, Thomas said.
He said the bacteria had become resistant to antibiotics because of both overuse and misuse of the drug.
Thomas said antibiotic resistance was a growing issue, but New Zealand hospitals were "cautious" when treating with antibiotics.
