Under the proposal, Concert would be taken off FM radio on May 29 and the youth platform would be phased in ahead of its full launch on August 28.
While Ardern conceded it was important for RNZ to make its own programming decisions, she noted that this extended beyond a programming issue.
The arts community, in particular, has been outraged by the move, given the station's role in playing and promoting classical music. Former Prime Minister Helen Clark has been among the most vocal critics of the RNZ move.
In comments made on RNZ's Morning report, Ardern spoke of the importance of ensuring access to the arts in New Zealand.
"I feel very strongly about this. When I came in as Minister for Arts, Culture and Heritage, one of the priorities I had was access - that we need to broaden the access of all New Zealander to the arts," she said.
"I understand that RNZ has obligations to all New Zealanders, and it is their view that they are not catering for one sector. But it is my view as arts minister that one does not need to come at the cost of another.
"My frustration here is I see that this beyond a programming decision into structural decision."
An RNZ spokesman said it was clear the broadcaster was not yet relevant to people in all their life stages and it failed to connect with some groups.
These included Māori, Pacific and Asian people and younger audiences.
"Music provides an ideal way of reaching those audiences that do not currently engage with RNZ and the new station will be unlike anything currently available from commercial networks."
He said RNZ was aware of the public feedback in relation to its music strategy and would continue to consult and take account of comments on these proposals.
RNZ did not directly answer questions as to why, when the Government had asked for more time before a decision was made, it went ahead with plans anyway.
READ MORE:
• Petition soars as opposition hardens against gutting of RNZ's Concert programme
• 'Killing a museum': Should RNZ stick with Concert?
• Former Prime Minister Helen Clark wants Ministers to scrap plans to ditch Concert FM
• RNZ shakeup: Is it curtains for Concert?
RNZ plans to replace Concert's FM slot with a youth-based station - which critics say would serve an audience already well covered by the commercial stations.
Ardern also hinted at tensions between the Government and RNZ management over the issue.
She said when Broadcasting Minister Kris Faafoi was briefed - very recently - on some of the proposed changes, he expressed concern and one of his clear concerns was over the loss of FM frequency for Concert.
"He explicitly asked for time so that we could see if whether or not there was something we could do to prevent the loss of the FM frequency for Concert. RNZ went ahead and announced this regardless," she said
"We tried to and asked for some time to explore and investigate how we could make sure that this wasn't an outcome that RNZ subsequently announced anyway.
"I'm pretty frustrated by that situation. It's unacceptable."
Ardern is set to make further comments on the move later today.
Protest march planned
More than 10,000 people have signed a petition calling on RNZ to ditch plans to gut its music station Concert.
Prominent New Zealand soprano Gina Sanders is also in the process of organising a nationwide march in opposition of the proposed cuts.
Sanders says the prospect of the changes to Concert FM will negatively affect all New Zealanders, but young people most.
"Nearly 10,000 secondary students compete in an annual festival, The Big Sing, that is unique in the world – RNZ has a massive part in broadcasting and livestreaming this national choir competition and the finale is broadcast on the FM frequency, which is highly accessible to all New Zealanders. It is also a springboard for additional festivals through the regions," she said.
"Also thanks to Concert FM, the Lexus Song Quest continues to enjoy high numbers in entries because it gives young people unprecedented access to the arts and culture. It is important to remember that Concert FM is not just for classical music; it has cutting-edge programmes in pop, rock, jazz and many other genres."
The national march to save Concert FM has gathered more than 1500 followers so far.
Organisers are planning at least 18 "cultural hubs" in cities and towns nationwide, meeting at midday on Friday, February 28.
- Additional reporting RNZ.