Travelling between their Taieri Mouth home and Taieri College, Mosgiel, costs their family more than $90 a week.
Although brothers Kayne (15), Shaun (16) and Josh (13) are zoned for the college, they must travel through Green Island, which is outside the school's subsided transport area.
Taieri College Deputy principal Paul Bolton said the school had approached the ministry several times about transport funding for several Taieri Mouth pupils and establishing a subsidised service which by-passed Green Island.
The ministry pays for the boys' transport from Taieri Mouth to Brighton, but from Brighton to Mosgiel they use public transport and school-contracted services, and pay for both, Mr Bolton said.
"We pointed out pupils travelling between the school and Middlemarch - a much greater distance - do so free, because the route is inside a transport zone.
Although [the ministry] is fulfilling its obligations, I think it imposed the boundaries and should provide transport for pupils," Mr Bolton said.
Kavanagh College principal Paul Ferris said "a handful" of pupils from the Otago Peninsula, about 20 from Port Chalmers and 20 from Mosgiel travelled to the Dunedin school using public transport each day.
"It disadvantages families who want access to an integrated Catholic school. When the ministry decided Port Chalmers was not eligible for free transport because it was inside city boundaries, money was available to administer a buffer subsidy.
"In 2003, that money ran out and parents now pay the full cost of transport. This can be over $20 a week per pupil and that's a major cost when really those children should be transported for free - it's an injustice," he said.
Mr Ferris contacted the Otago Regional Council in March after a run past the school, which linked with services to Port Chalmers, was discontinued.
Pupils were now dropped in Cumberland St, in central Dunedin, and were not guaranteed places on busy morning buses.
"[Pupils] have taken digital cameras to show how packed it was. Kids have been left behind. And during the cruise-ship season when passengers use the cheaper and regular [public] bus service, there's even less room. It has been a nightmare for kids from Port," he said.
The Anderson boys' father, Duncan, said the boys could drive about 20km inland to Henley and get a free bus to the college, but they held only restricted car licences.
"Everyone I've told the story to is amazed there's no assistance."
