A Palmerston school that decided to shave 10 minutes off every hour it paid a casual relief teacher has found itself facing a bill for thousands of dollars of historical underpayments.

Anne Thompson told RNZ East Otago High School's penny-pinching prompted her to look into her rights and discover it had been under-paying her for years.

She said her investigation began after the school decided earlier this year to pay her for 50 minutes instead of 60 minutes for each class she covered.

Thompson said the extra 10 minutes covered non-timetabled duties like finding which classroom she would be working in, collecting the classroom key and finding the work to set her students.

"They've always paid for 60 minutes even for a 50-minute lesson and this year they decided they were going to start paying 50 minutes," she said.

"I was told they were doing it to save money."

Thompson said she felt that was unfair because she easily spent 10 minutes organising keys and paperwork for each class she taught at the school.

When she looked into her rights, she found the school had been under-paying her for the entire three-and-a-half-years she had been working for them.

Thompson said the school had failed to provide an hour's pay in situations where the gap between her hours of work was 90 minutes or more.

"I discovered on the collective agreement that I should have been being paid when there were these big gaps in my day, which I often had," she said.

A document Thompson shared with RNZ showed the school last week agreed it owed her 34 hours of backpay going back to 2022.

But Thompson said she calculated the shortfall was about 58 hours including instances where her rate was calculated at 50 minutes per class, and some classes she was not paid for at all.

"I worked at the school for three years and nine months and they were under-paying me throughout that time. It's just under $5000 that they owe me," she said.

She said she had decided to stop working for the school and this week lodged a personal grievance.

Thompson said she shared her experience on a social media group for relief teachers and some said other schools had also failed to pay for an hour of work when the gap between classes was 90 minutes or more.

RNZ asked East Otago High School to confirm Thompson's claims.

Principal Helen Newcombe told RNZ it could not disclose information about its employees' salaries and entitlements.

"When employees raise issues with us regarding their entitlements under the Secondary Teachers' Collective Agreement, we ensure that we work alongside the Ministry of Education to resolve concerns and to meet all of our legal obligations," she said in a statement.

The Education Ministry said school boards were responsible ensuring their schools adhered to collective agreement employment terms.

"If an employee has a concern about their pay, they should raise this with the school in the first instance," it said.