The Ministry of Education says there is no room on school buses for physical distancing when services resume under lockdown level 2.
It's blaming a shortage of drivers and buses for preventing it from putting on additional services to give students more room from each other.
Back to school will mean packed school bus trips for many students.
The Ministry of Education says it was not possible to source more drivers and for children on buses to maintain the physical distancing required in most other sectors of society. But Dunedin Tramways Union president Peter Dowden said this is rubbish.
"We're aware of hundreds of buses being put into storage in the tourism and sightseeing sector of the industry and hundreds of drivers have lost their jobs."
He said drivers would have welcomed the work and it did not look like the ministry even attempted to put on more services.
"The point is they should at least be trying, they should at least have as much physical separation as is practicable, that's what all the rest of the country is doing.
"I don't know why the Ministry of Education thinks that school buses don't matter, or school children don't matter."
Northland father Giles McNeill said he was concerned for the health of his five-year-old daughter and will not be putting her back onto the bus any time soon.
"My worry about it is, that it's a bit of a sardine situation and we don't know any of the other sardines, you know, most of the kids on that bus happen not to go to her school - so it's just introducing a huge unknown factor and that's the danger."
The Education Minister has acknowledged that it is almost impossible for children to stick to physical distancing rules, so the emphasis is on good hygiene and contract tracing in schools.
Kevin Bush, the principal of Te Hihi school south east of Auckland, said these same factors applied to the school bus run. He said he had to have faith in officials' advice that young people were unlikely to pass on the virus.
"They are confident you know that COVID-19 won't be spread across the school bus network and so we have to share in that confidence really."
Auckland Secondary Schools Principals' Association president Steve Hargreaves said cramming students onto school buses was risky and parents have contacted him with their concerns.
He also saw another big problem looming, with public transport in cities like Auckland and Wellington running at about 40 percent capacity due to physical distancing rules.
"I can see a potential disaster with our students trying to get to school using public buses and if they're going to reduce the capacity to accommodate physical distancing then we're going to have hundreds of kids being left on the roadside not being able to get to school."
The Ministry of Education said in a statement the risk of students spreading COVID-19 can be mitigated with extra cleaning, and it will supply hand sanitisers for drivers and students to use.
It said it will be schools' responsibility to keep accurate passenger lists to allow for contract tracing.