They are calling for DHBs and hospitals to develop a nationally-coordinated response plan to deal with the threat.
In New Zealand most people with CPE are believed to have been infected overseas, especially on the Indian subcontinent.
But specialist in clinical microbiology Dr Joshua Freeman told Newstalk ZB there were now several cases of probable secondary spread in hospitals.
Freeman said the way to address it was to try and identify people who may be carrying the bacteria and put in place measures to prevent further spread.
People who carry CPE may have them only for about three to six months, he said.
Patients undergoing procedures such as transplants or cancer treatment are particularly reliant on antibiotics and are most affected by the threat of CPE.