Many school support staff are this year suffering from lower than usual pay checks because of a pay cycle anomaly - forcing a teachers union to take the case to the Employment Relations Authority.

Support staff at schools are generally paid for 40 weeks of work, which they can choose to "annualise" by spreading out their salary over the full 52 weeks of the year, or 364 days.

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With 365 days in a normal year and 366 in a leap year, this means there are days left over each year. Every 11 years, an extra fortnight is added to the pay cycle to account for the leftover days, happening this year for the first time since annualisation was introduced in 2006, which means affected staff are having their salary stretched out over a longer period of time.

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Teachers' union New Zealand Education Institute (NZEI) is taking the issue to the Employment Relations Authority next month, saying the changes to pay checks breach its collective contract. The NZEI estimated affected staff were getting 3.7 per cent less pay per fortnight.

Jan Tinetti, principal of Merivale School, said the change was "unfair" on employees crucial to schools.

"These guys do an amazing job, we can't run schools without them. It's just not fair."

Ms Tinetti said it was not good enough for the ministry to say they notified staff in November. She said it came out of the blue and people did not immediately understand what it meant.

These guys do an amazing job, we can't run schools without them. It's just not fair.

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"Our support staff are absolutely critical at this school. I couldn't run the school without them. Yes, they might get the full amount over the year, but you budget week to week to pay your rent and pay those costs. That's why it's not fair."

Greenpark School principal Graeme Lind said he supported the support staff and their claims. Mr Lind said he would like to see a system where teacher aides were paid by the Government like teachers were, instead of schools having to pay their wages out of school operations grants.

Ministry of Education head of education infrastructure service Jerome Sheppard said the staff still got the same total annual pay, just at a slightly lower rate each fortnight.

"Staff who choose to have their pay annualised still receive their full pay and entitlements. Everyone is paid for the hours worked, at the rates set out in their agreements."

Mr Sheppard said annualising pay was "entirely voluntary" and that staff were notified of the change in November.

- Additional reporting NZME