"Given the possibility that Zika virus can cause severe malformations inunborn babies, and taking a very cautious approach, pregnant women should discuss any travel plans with the travel doctor and consider postponing travel to Indonesia," a statement from the department said.
The warning advises travellers to Indonesia to protect themselves from mosquito bites.
Travel Doctors' Jennifer Sisson told the NT News the risk of transmission in Indonesia was relatively low, but not non-existant.
"There might be an odd case here or there but they're not having an actual outbreak," she said.
"Sporadic transmission means from time to time there is a case but it's certainly not an outbreak like Brazil."
The Ministry of Foreign Affairs and Trade (MFAT) has not issued a specific warning for New Zealand travellers to the country and its Indonesia travel advice was last reviewed in January.
MFAT advises those travelling to affected areas to protest themselves against mosquito bites and consider delaying travel for pregnant woman, or those who plan to become pregnant.
Men who have travelled to a Zika-affected area are advised to avoid sex or use condoms, even when symptoms to not present.
49 countries are now listed as having current or recent transmission of the virus, including Brazil, Samoa, Tonga and Vietnam.
