Ardern said she still does not agree with the deportation policy but she questioned whether it was appropriate if a minor was involved.
She said she would have expected care to have been taken if a minor was involved.
The situation would have been something officials would have been aware of but she does not get a breakdown each time people were deported, she said.
"At this point, those who need to know do," she said on the issue.
An Oranga Tamariki spokesperson said the agency has been working extensively with the relevant authorities in Australia and New Zealand to support the boy's arrival into New Zealand.
"He is currently in a managed isolation facility and receiving support while undertaking quarantine."
It comes after Australian Home Affairs Minister Peter Dutton was quoted in a 9 News report saying the deportation process was Australia's way of "taking the trash out".
"We're talking about the most serious offenders here and our country is safer for having deported them," he said.
Foreign Affairs Minister Nanaia Mahuta said Dutton's comments "only serve to trash his own reputation".
"I think they should reflect on how they are portraying the transfer of people back to New Zealand."
Minister for Covid-19 Response Chris Hipkins also slammed the comments and the Australian deportation policy in general - which is not reciprocated by New Zealand.
"This is a deplorable move by the Australian government and we completely disagree with it, however they are entitled to do it."
