"Failure to act now will significantly harm the health of our population in the future."
Resistance to commonly used antibiotics in a wide range of bacteria that were responsible for common diseases was rapidly emerging as a major threat to health, Dr Thomas said.
For most infections due to antibiotic-resistant bacteria, a relatively effective treatment was available, even if it had disadvantages regarding cost, convenience or adverse effects, he said.
"If untreatable infections from drug-resistant organisms become common here, this will have major consequences for the New Zealand healthcare system."
In the seven years from 2005 to 2012, the increase in using antibiotics by patients increased by 43 per cent - an average annual increase of just over six per cent each year.
The low rates of completely drug-resistant organisms in New Zealand meant the infectious risks of some modern medical procedures, such as organ transplantation, joint replacements, and prolonged stays in an intensive care unit, were considered acceptable for most patients, Dr Thomas said.
"If an increasing proportion of procedure-related infections are caused by untreatable bacteria, the infectious risks may be considered less acceptable and the use of these procedures curtailed.
"Increasing antibiotic resistance threatens a very wide range of medical and surgical practices," Dr Thomas said.