Prime Minister Jacinda Ardern said New Zealand had a choice when it came to the return of Suhayra Aden - who had alleged links to ISIS - and her children.
"Either Turkey would repatriate without New Zealand having the ability to plan for that properly, or we accept that we have an obligation."
Ardern said this obligation was undeniable "given that this is a New Zealand citizen".
"Making those plans we can ensure we have the safety considerations of New Zealanders as our highest priority," she said.
"A lot of work has been done over the past few months to make sure this is done safely with the community particular in mind."
Police today confirmed an investigation is underway, but would not comment further on the situation.
Aden had dual New Zealand-Australian citizenship, however, her Australian citizenship was stripped by Scott Morrison's government, causing Ardern to heavily criticise the decision earlier this year.
Today, Ardern reiterated that it was frustrating, saying New Zealand did see the situation as "Australia's obligation".
"They took a different view, they arbitrarily cancelled the citizenship of the individual involved."
On communications with Australia, Ardern said she had been given an explanation by officials and leadership.
"I just don't accept it."
However, New Zealand had been given assurances from Australia it would "simply not happen again".
"The choice of not accepting a repatriation could well have led to Turkey to have the person shipped back to New Zealand without any safety contingency, that would not have been right for us or for the children involved."
"These are children who through no fault of their own are in dire circumstances, at the same time we are absolutely committed to preserving the safety of New Zealanders."
When asked about the situation earlier this year, Morrison said it was his job as Australian Prime Minister "to put Australia's national security interests first".
He said laws passed in Australia automatically cancel the citizenship of a dual citizen "when they’ve been engaged in terrorist activities of that nature".