About 20% of New Zealand schools use the scheme under which boards of trustees - not the ministry - administer transport contracts in accordance with ministry rules.
Boards must ensure vehicles meet safety, emissions and maintenance standards and that drivers are adequately trained.
Scheme funding also applies to schools which own their own buses and employ drivers directly.
While the ministry stresses the programme is optional, some Otago school leaders are concerned the directly resourced package could become mandatory, with one school chief executive comparing the scheme to bulk funding for teachers' pay, which was widely rejected last year.
Taieri College deputy principal Paul Bolton said more than 150 pupils travelled to and from the college on six bus runs each day.
"We looked at the scheme earlier this year for potential savings. If costs were set, and say fuel increased, we have to wear it. The whole concept of having another administrative level was frightening."
The school operated one "user-pays" bus run which the ministry partially funded because of zoning limitations and the limited availability of public transport.
School services manager Mel Tudor said the school investigated the scheme in case it gave greater flexibility for bus routes.
"There did not seem to be guarantees in place to guard against increases like labour costs for drivers. It seemed to follow on from the Tomorrow's Schools concept for schools having greater autonomy with things like bulk funding for teachers."
Transport operators the school had spoken to said the cost of operating routes could be "double the $1.89 per km offered by the ministry", he said.
Catlins Area School principal Gavin Kidd said about 110 pupils travelled to school by bus each day.
"We looked at the scheme, but are in a situation where there is one local bus company, so wouldn't save through competition for the contract - and we are very happy with the service they provide.
"Schools are busy enough and schemes like this seem to be a means of the ministry decreasing responsibility long term.
"We definitely had the feeling they were giving responsibility back to school on the assumption they were in a position to handle the extra work."
Kavanagh College principal Paul Ferris, of Dunedin, said he was not aware of any Dunedin school intending to adopt the scheme.
"It is not a goer here. Schools are not afraid of administering special education grants, such as bulk operational funds, if there is an advantage, but there would have to be huge incentive to take on the administrative burden.
"In Dunedin, the placement of schools means they share runs and there's a shortage of buses and drivers.
"Boards would also be worried about ways to cover increased costs like fuel," he said.
"It's interesting the one thing the ministry wants schools to self-manage is something they don't want to do themselves. Managing transport is not part of the core function of education providers," Mr Ferris said.
In December 2007, Cabinet approved increases to the scheme's funding formula and introduced more stringent safety standards for contractors.
From January next year, schools in the scheme will receive a base amount of $60.81 per route, $1.89 for each kilometre travelled and a quarterly administration fee of $176.
Consultation for a new memorandum of agreement between boards and the ministry closed on July 25 and submissions are being analysed.
The finalised agreement was distributed to school boards in August and changes will be implemented in January next year.
During consultation, input was sought from industry groups, including the New Zealand School Trustees Association, Rural Women New Zealand, the Office of the Auditor-general, the Bus and Coach Association and Land Transport New Zealand.
In a recent article for the New Zealand School Trustees Association, the ministry said boards using the scheme might be able to use local knowledge to contract services at a cheaper rate than the ministry, to provide transport for ineligible pupils, or to develop bus routes more suited their school zones.
