Kea are protected by law, and under the Wildlife Act killing one is a criminal offence that carries a maximum fine of $100,000 or six months in prison. It is believed there are fewer than 5000 kea left in the Southern Alps - the only place in the world where they are found.
Porter Heights Ski Area manager Uli Dinsenbacher said the death had "upset" his staff, who adored the cheeky kea population that inhabits the area.
None of his staff saw the incident, and while he said the children were well-behaved on the slopes, he was disgusted by it.
"It's something we feel very strongly about," Mr Dinsenbacher said.
"But we can't be held responsible for kids outside lesson times who are roaming around getting into trouble."
DOC field centre supervisor Chris Stewart said the "horrible" death was also unusual, having never come across anything similar before.
The corpse was taken away by school staff and would be delivered to DOC's Christchurch office tomorrow where officers will speak with the school and the boy to discover what happened.
Mr Stewart said, "Once we gather all the information, we'll see the level of culpability he has, find out what his reasons were, and take it from there."
DOC has jurisdiction and power to investigate and prosecute any wildlife crime themselves, without referring the case to police.
Forest and Bird conservation advocate Nicola Toki said while the incident was "sad and disappointing" it highlighted a wider issue over a lack of education.
"If we're in a position where kids are throwing stones at a beautiful, endangered, intelligent, and cheeky species, then there's a gap in knowledge about our incredible wildlife."
Tamsin Orr-Walker, of Kea Conservation Trust, said kea are not only endangered but particularly trusting animals.
"I hope it wasn't intentional but just a silly mistake," she said.
"We have loads of kids contact the trust who are are really keen to protect the kea and they will be horrified to hear of this."
Chisnallwood Intermediate, meanwhile, was apologetic over the death.
Richard Paton, school principal, said while the boy simply picked up a rock and threw it at the highly-intelligent bird, he didn't think there was any malice in the event.
"I think he was as shocked as anybody that it actually hit the kea, and that it died," Mr Paton said.
"The boy involved is very remorseful, but there will be some consequences for his actions.
"The other students on the trip were as upset as anybody and they also feel let down by the mindless actions of one person.
"It's unfortunate that the actions of one person can reflect badly on the school."
Last August, five young kea were found shot dead at Klondyke Corner, near Arthur's Pass.
They were found piled up on a picnic table, but despite a DOC investigation, the killers were never found.
