The New Zealand government has agreed to the managed return of a New citizen and her two young children from Turkey, Prime Minister Jacinda Ardern said on Monday.

The three have been in immigration detention in Turkey since crossing the border from Syria earlier this year, reports Xinhua news agency.

The Turkish government identified the New Zealand citizen Suhayra Aden as a terrorist belonging to the Islamic State (IS), and has requested that New Zealand repatriate the family.

"The safety and wellbeing of New Zealanders is paramount for the government," Ardern said in a statement, adding New Zealand has not taken this step lightly.

"We have taken into account our international responsibilities as well as the details of this particular case, including the fact that children are involved," she said, adding the woman was a dual New Zealand-Australian citizen until Canberra revoked her citizenship.

"Unfortunately, Australia would not reverse the cancellation of citizenship," Ardern said.

"A number of other countries have managed the return of mothers and children from the region and this is the position we now find ourselves in," she said, adding in this case the welfare and best interests of the children has been a primary concern.

It has previously been made clear that any New Zealander who might be suspected of association with a terrorist group should expect to be investigated under the country's law, but that would be a matter for the Police, Ardern said.