The ministry announced last week that the introduction of a revamped public bus network next month, featuring a $2 flat fare, meant it could no longer justify its funding of the school bus service.
Mr Boult said the move would flood the new network with school children, undermining its purpose of reducing congestion by getting residents out of their cars.
''The last we want to do is swamp it with students and put commuters off using it.
''At a point in the future, the service may develop so it can handle school children, but at this stage, let's get it up and running successfully.''
He disputed a claim by the ministry's head of education infrastructure service, Kim Shannon, that the new network had been ''specifically designed to cater to students' needs'' and was ''targeting the student market''.
Mr Boult said that proposition had not figured in any discussions between his council and the Otago Regional Council (ORC), who are jointly funding the network with the NZ Transport Agency.
ORC support services manager Gerard Collings confirmed to the ODT through a spokeswoman the new network was ''not targeting the student market''.
Mr Boult said he wrote to Education Minister Nikki Kaye last week asking for the decision to be reviewed, but had yet to receive a response. It was now clear he needed to take up the matter with the ministry directly.
Ms Shannon said the ministry's eligibility criteria for funding school bus services were applied equally throughout New Zealand, and Wakatipu was not the only region where communities were scattered and children faced challenges walking or biking to school.
Asked if the Ministry would consider delaying the change for one or two years to allow the new bus network to bed in, she said the decision had already been on hold for some time.
''We initially met with the Queenstown school community in 2013 about our concern that school transport assistance was being provided when public transport was available for use.
''A decision to stop ministry services where public transport was available was delayed to allow more time to make sure genuinely suitable services were available for those affected.''
Pupils would remain eligible if they attended the closest school they could enrol at, lived at least 3.2km (years 1-8) or 4.8km (year 9 and above) from that school and no public transport was available, she said.
Mr Boult said he had received a ''massive'' amount of feedback from parents in the past week.
Not only was the Ministry ''dumping'' the cost of transporting school children on the district's ratepayers, families would have to pay $15 a week for every child that used the public network.
''That's quite a lot of money for ordinary families.''
He was also concerned about the safety of younger children attending Queenstown Primary School.
''If you're a family up in Fernhill and your child comes down on a school bus and gets deposited at O'Connells [shopping centre], a 5 or 6-year-old has to cross two busy roads to get up to the school.
''Personally, I wouldn't be happy if that was my child.''
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What is the fuss? it is what many urban families of school children have been paying for years and as the article said - notifications since 2013. Times have changed since the school bus system was first brought in.