Counties Manakau district crime manager Tofilau Faamanuia Vaaelua gave the grisly update on Thursday, while confirming the homicide investigation had broadened to involve international agencies.
The remains were discovered earlier this week by a family who purchased the contents of an abandoned storage locker in South Auckland at auction.
Police say the family are "understandably distressed" by the find and are not connected to the deaths of the children.
Acknowledging the update would be "extremely upsetting for the community", Mr Vaaelua said police believed the remains were of two children aged between five and ten years old.
"Early indications suggest these children may have been deceased for a number of years before being found last week. We also believe the suitcases have been in storage for a number of years," he said, later suggesting the children's remains may have been stored for three to four years.
"It's still very early stages of our investigation. We're still on a fact-finding mission and we still have a lot of unanswered questions."
The remains were found in two similar-shaped suitcases.
Neighbours, including a crematorium worker, have told local media of a "wicked smell" in the area last Thursday aligning with when the remains were identified.
Police are working on a formal identification process and Mr Vaaelua said the priority is to contact the next of kin.
Police are trawling through the rest of the items in the storage locker to establish links and to try to identify the remains.
Mr Vaaelua declined to answer whether police believed the children were related, or questions about their gender or the state of the remains.
"That information is very important to the investigation and I'm not prepared to comment on that," he said.
Local media have suggested overseas links to the case though, again, Mr Vaaelua was tight-lipped.
"All we can say is there are relatives of the victims who are in New Zealand," he said.
"We're working with Interpol and we've commenced inquiries with overseas agencies."
The crime has rocked New Zealand and particularly the Manurewa community in South Auckland, home to strong Maori and Pacific populations.
"I really feel for the family of these victims," Mr Vaaelua said.
"Right here, right now, there are relatives out there that aren't aware that their loved ones have deceased, especially two young children.
"This is no easy investigation. No matter how long or how many years you serve and investigate horrific cases like this, it's never any easy task."
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