A problem is cutting the fortnightly pay of thousands of school support staff this year, the New Zealand Educational Institute (NZEI) says - and it is taking the Ministry of Education to the Employment Court over the matter.

The union said about 6000 staff were receiving 3.7 percent less in each pay this year because of a calendar anomaly.

Photo: RNZ / Diego Opatowski

Staff are due a catch-up pay in February next year, but the union's national secretary, Paul Goulter, said the reduction in their regular salary was too tough on an already low-paid group of workers.

"Given the low wages that these support staff have, that's significant and significant economies are having to be made by people who shouldn't have been exposed to what we believe is an unlawful cut."

Mr Goulter said the union was told the school payroll system was to blame.

"We've been told it's a Novopay problem and all of our discussions have been around 'Novopay can't do this'.

"Novopay couldn't even pay teachers and support staff properly so this is just another woeful story of a really bad pay system."

But the head of the ministry's education infrastructure service, Jerome Sheppard, said the method of payment had nothing to do with Novopay.

Annualising pay was not new and was entirely voluntary, he said.

"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," he said.

"What is different this year is that there will be 27 pay days, rather than the usual 26, because of the way payroll dates fall in the 2016/17 tax year. This means that staff pay will be slightly lower each fortnight, but there will be an extra pay cycle which will bring the total annual pay up to the same amount."

Mr Sheppard said staff were contacted in November and given until 25 January to decide if they wanted to annualise their pay in 2016.

"More staff chose to annualise this year than last year," he said.

But one of those affected by the problem, Susan Renshaw from Aotea College in Wellington, said staff did not get enough information about the change.

She said the cut to her pay was making it hard to pay the bills and the catch-up pay in February was no consolation.

"February's what, 11 months away? It doesn't help. If the ministry or whoever is deciding that that's when it's going to happen, maybe they could ring Spark and Genesis and New World and tell them, 'don't worry they'll pay it in February'."

Ms Renshaw said her colleagues who had chosen not to annualise their pay this year were running out of money in the holidays when they were not being paid.

NZEI said it had not been able to reach agreement with the ministry over the issue and would take the case to the Employment Court in April.

Novopay not responsible - Joyce

The Minister responsible for fixing Novopay, Steven Joyce, said the NZEI was being mischievous by blaming the payroll system for the problem.

Photo: RNZ / Alexander Robertson

"It's actually an issue related to the calendar year being a 366 day calendar year and the way the fortnights fall there are 27 fortnights in the year, normally there's 26. So it's not a Novopay issue, it's not an anything issue except that if you have an annualised pay it goes out over 27 fortnights instead of 26."

Mr Joyce said he understood people were finding it hard to make ends meet, but the affected staff were clearly told about the problem in October last year.

"Staff were advised when they were asked to seek annualisation or not last year that it would be 27 pays this year and therefore a slightly lower amount per pay, and 6000 in the knowledge of that chose to take up annualisation."

Mr Joyce said the problem would occur again.

"It will happen again in 11 years, no matter who the payroll provider is unless somebody elects annualisation to be taking one less fortnightly pay and just missing out at the end of the year, and I don't think anybody would be in favour of that."