A Manawatu teacher who returned the $39,000 she was overpaid by Novopay has not been paid since.

And a first-time principal says she threatened the Education Ministry with quitting her job in her frustration at the beleaguered electronic payroll system's blunders.

Principals of small Manawatu schools invited to attend a Novopay training session in two weeks' time say they are scrambling to find relief teachers to cover the day off, with some teachers refusing to attend.

Apiti School principal Mary Cumming said she would struggle to find the time to attend the November 12 workshop.

She was notified of the event on Thursday evening.

"They should be paying us for a reliever and the day off," she said.

"Where are small schools going to find a reliever at this time of year at such short notice?"

Mrs Cumming said one of her two staff members who returned the $39,000 she was overpaid in one pay cycle in September has not been paid since.

"We should just drop everything and just come to a bloody Novopay workshop?

"I think they have cheek."

Bainesse School teaching principal Andrea Harnett said she had threatened to quit over the payroll system blunders.

"It has been an absolute nightmare for me. I'm so lucky to have the staff that I have."

She did not plan to attend the scheduled Novopay seminar - an inter-school athletics day planned for months would take precedence.

Kiwitea School teaching principal Dirk Jochem said small schools like his had not been given enough notice about the seminars.

"So Novopay thinks it can just send us an email saying come do some training? Yeah, right."

Waituna West school teaching principal Glen Richardson said he would prefer Novopay staff visited small schools to train staff, calling the system a "disaster".

A copy of an email provided by a Manawatu principal shows Wellington schools were given just one day's notice of the ministry training roadshow, with the first workshop held yesterday.

Post-Primary Teachers' Association general secretary Kevin Bunker criticised the ministry and Novopay owner Talent 2 for "an appalling lack of notice".

"It shows very little understanding of how schools work and smacks of last-minute planning," he said.

"Schools need to organise for teachers to be freed from the classroom to attend these sessions and that is no small thing."

A statement released by the Education Ministry said that it was pleased with the turnout at Wellington's Novopay day.

Group manager Rebecca Elvy said the purpose was to help schools get ready to use Novopay during the critical end-of-year and start-of-year payroll periods, and to share tips.

"We've been really appreciative of the time and effort payroll administrators and principals have put in during these first weeks of Novopay's implementation," she said.

An Education Ministry spokesperson said they accepted the notice period was very short for some schools, and apologised saying they needed to run the roadshow as soon as possible before the end-of-year pay period started.

Novopay has been plagued with problems since it was introduced this year.

As well as non-payments, there have also been issues with third-party payments such as superannuation and student loans being deducted from staff pay, but not paid to the various providers. Relief teachers and other staff who use timesheets have also suffered.

- © Fairfax NZ News