Foreign Affairs Minister Nanaia Mahuta was notified about the boy who would be deported to New Zealand by the Australian Government "some weeks ago".
But she has warned people not to assume the 15-year old minor was a 501 deportee.
Both she and Deputy Prime Minister Grant Robertson wouldn't elaborate much on the situation other than to say it is "complex".
This comes as the Green Party ramped up its attacks on the Australian Government, with its foreign affairs spokeswoman Golriz Ghahraman saying the country is behaving like a "rogue nation".
And National leader Judith Collins said: "I've never seen Australia and New Zealand relations at such a low ebb."
The situation is the worst it's been since the Muldoon government, she said this morning.
Yesterday, it was revealed that a 15-year-old boy was deported from Australia to New Zealand, along with a number of other Kiwis with convictions.
Speaking to media before going into the House this afternoon, Mahuta suggested the boy was not a 501 deportee despite the fact he was travelling on a plane with others in that category.
The Australian 501 policy means that "foreigners" can be deported from Australia if: They are seen as a risk to "health, safety or good order of the Australian community"; they are believed to be "not of good character", or if they have certain criminal convictions.
"I don't think we should jump to the conclusion that this is a 501 issue," Mahuta told media.
According to information provided to RNZ by Australia's Department of Home Affairs, no comment could be made on individual cases.
But, in a statement, the department said there were a range of circumstances under which someone could be deported.
"A non-citizen's visa must be cancelled if they are serving a full-time term of imprisonment for an offence committed in Australia and they have, at any time, been sentenced to a period of 12 months or more imprisonment, regardless of their age or nationality."
The statement also said: "Non-citizens who do not hold a valid visa will be liable for detention and removal from Australia".
The statement did not, however, say which one of these situations applied to the minor in question.
The department had approached visa cancellation of minors with a "high degree of caution and consultation" and "complies with its legal obligations in circumstances where the removal of a minor is considered, including those under the Convention on the Rights of the Child".
This morning, Robertson was clear that the boy "shouldn't have been on a plane with those other people who were being deported".
"It was not appropriate.
"In general, the issue of minors being deported is not one that we should be seeing."
Mahuta said that she was first notified of the boy's existence on February 19 and was notified that he would be sent to New Zealand on March 10.
Aside from that, Mahuta couldn't say much about the issue other than it was complex.
She said that Oranga Tamariki has been engaged in the process as soon as it arose as the "care of the child was a very important concern".
There were "some complex family issues around this matter".
She would not say if he had ever lived in New Zealand but he has family in Australia and New Zealand, Mahuta said.
"We have worked with the relevant Australian child authorities, as well as Oranga Tamariki on this."
Collins said the Australian Government sending the minor over was "really quite bad actually".
"A 15-year old has no doubt been involved in something they shouldn't have been involved in – but you have to be human."
She said in New Zealand, some 15-year olds get "some leeway" when it comes to behaviour unless it's extremely serious.
"It's a pretty tough call."
She said the rhetoric between Australia and New Zealand has been "rarking up" at the moment.
Collins was also critical about Home Affairs Minister Peter Dutton's "taking out the trash" comments about the deportees.
"It speaks a lot about the lack of goodwill I'm seeing at the moment [between Australia and New Zealand.]"