It planned to withdraw the vast majority of school bus services after the resort's much-heralded $2 bus service became operational on November 20.
The resort would no longer meet the criteria for state-subsidised school buses due to the expanded public transport network, except for more rural areas.
But Queenstown Lakes District Council, Queenstown's Mayor Jim Boult, and the Otago Regional Council complained the change could overload the new network in its infancy.
Last week, all parties, including Wakatipu High School met for discussions.
Peter Bodeker, Otago Regional Council Chief Executive, said: ''From those discussions, it has been agreed that Ministry services will continue for Arthurs Point, Arrowtown, Lake Hayes Estate, Quail Rise, Shotover Country, as well as those areas currently serviced by the Ministry outside public transport routes.''
This would be until the public services could provide the necessary frequency, capacity and timing for this purpose.
But some high school children will be required to use the public network.
The ORC will have services available to transport high school students currently using Ministry School buses from Sunshine Bay, Frankton, Jack's Point and Kelvin Heights.
Mr Bodeker said the possible need for additional passenger capacity on the Fernhill-Remarkables Park service had been identified.
The new Wakatipu High School is due to open at Remarkables Park in January.
Regional council staff would investigate this further, and report back to councillors.
Mr Boult acknowledged the agreement between ORC and the Ministry as the ''right, common-sense decision for the local community'', a press release from ORC said.
''This is a great result for both students and families of the Wakatipu," Mr Boult said.
''Having clarity around how our students are getting to and from school is something we have all pushed hard for and it's fantastic to see a sound approach to the issue being taken.
''It also gives the new $2 bus service the opportunity to really get off the ground with local commuters and visitors.''
The Ministry will continue to work collaboratively with Otago Regional Council and the local schools on finding appropriate school transport solutions to help students further integrate with the developing public transport network, the release said.
ORC chairman Stephen Woodhead said: ''I know there has been a lot of concern among parents and teachers in Wakatipu about the future of these services, and we are pleased to be able to provide greater clarity.''
