NZTA said it had never come across the issue before and was looking into the problem.
Members of the school’s Enviroclub Chloe Spooner, 10, and Xan Wolsink, 9, found more than 20 bees either dead or about to die on Thursday morning.
They said the road outside their school (State Highway 88) had been sprayed with pesticide the night before and they suspected that was what killed the bees.
Xan said he was was playing barefoot when he nearly stepped on a dead bee.
"There are only a few of them and they’re probably all just dead too."
He was worried the bumblebees would poison the honeybees in their hive and was scared that would affect their business, Schoolgate Greens.
Chloe said they cultivated little plants for the community as well as vegetables such as rhubarb, herbs and peas.
She was worried the produce would be affected and the honey they produced would go bad as well.
The pupils did not want any pesticide sprays to be used in their area, Chloe said.
The pupils suspected the honeybees might also have been poisoned.
Otago Polytechnic Apiculture principal lecturer Dr David Woodward said it was highly likely if pesticide had been sprayed near the school, that was what killed the bees.
"It sounds like if the bumblebees are dead then almost certainly it would be the pesticides that would have done that," Dr Woodward said.
It was possible the forager honeybees had also been poisoned by the pesticide.
He was not totally against pesticide use.
It would be OK to use it late in the evening and early in the morning.
He said it was an unfortunate situation but it was possible just the foraging bumblebees were affected and the rest of the bumblebee nest was all right.
"The bumblebees might have survived long term," he said.
An NZTA spokesman said it was going to discuss with its contractors who provided the spraying service to better understand if there was potential for any harm to the bumblebees.
