One route will be cancelled, a new route will be introduced, seven will be redesigned and the remaining 11 routes will continue on an interim basis.
The ministry has warned parents most services will be scrapped where "suitable" Otago Regional Council-provided public transport already exists.
In a media statement, council regional planning and transport general manager Anita Dawe said the interim routes would "help maintain capacity on the network".
However, based on its understanding of the number of students impacted when the interim routes would be discontinued, the council believed "there is currently not enough capacity on the public network at peak times".
Ms Dawe said the council expected to receive requests from schools not on public bus routes to redesign routes or introduce special school bus services.
However, it would not be able to do so because of financial constraints as well as a lack of buses and drivers.
Wakatipu High School principal Oded Nathan said the ministry had recognised the council did not have the capacity to cope with the increased demand if it cut most of the school bus routes.
"So, they’ve agreed they’ll continue to run the vast majority of the buses, including some additional ones, in term 2, but that will not be indefinite."
The ministry had also said it would change some bus stops to get them "aligned with where the council would eventually have them", Mr Nathan said.
Queenstown Primary School principal Fiona Cavanagh said he school would lose the Sunshine Bay/Fernhill bus route, but the Arthurs Point school bus route, which was shared with St Joseph’s School, would continue.
The Mount Creighton/Bob’s Cove route would also continue, because there was no public bus available for those children.
Ms Cavanagh said she wanted that bus to also pick up students from Fernhill and Sunshine Bay, because it went past that area.
She was also pushing for public buses carrying students to make drop-offs and pick-ups outside her school.
— Philip Chandler and Guy Williams
