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The number of errors made by the Ministry of Education's Novopay system has leapt from 490 to 3227 in two weeks.
During question time a fortnight ago, Associate Minister of Education Craig Foss said 100 teachers were either not paid or underpaid during the last pay cycle and 390 teachers were overpaid.
Today in question time that figure was raised to 3227.
The figure includes a backlog of mistakes with the first two pay cycles including salary assessments for people joining payroll, changes of address or bank account, and extra allowances for bus controllers, management units, maternity leave and after-school coaching.
Mr Foss said all errors would be resolved by the end of the week.
Labour's education spokeswoman Nanaia Mahuta called on the ministry or its payroll provider Talent2 to compensate schools for the time and money they had spent fixing payroll mistakes resulting from the Novopay system.
Mrs Mahuta also called for teachers to be compensated for any penalties they incurred from not being paid.
Mr Foss said the ministry had not decided on if it would compensate schools or teachers for the costs involved with mistakes on the Novopay system.
"We're focusing on making sure Novopay is implemented and operating correctly, as intended and as contracted to with Talent2."
Primary school principals started invoicing the Ministry of Education today for extra hours staff have spent focused on sorting out errors.
And principals at schools in Auckland and Wellington say they will refuse to take on any extra work from the ministry until the problems with Novopay have been resolved.
Sacred Heart principal Lisl Prendergast said one of her staff members had been overpaid by $9000 and she knew of two schools that opted not to deal with the ministry.
"There are two colleges I know of where people are very unhappy, and in order to protect the executive officer the principal has said simply 'don't deal with the ministry until it's sorted - just get on with the rest of your job'."
Auckland Area Council principals' reference group members Malcolm Milner and Frances Nelson said principals wanted to prioritise leading teaching and learning over administration.
"Because of the hours spent on the Novopay shambles we must prioritise work that is about directly supporting student learning," they said.
Secretary for Education Lesley Longstone said Talent2 would be providing training to school staff to help address issues with its new payroll system. The ministry would also extend its Novopay road show which was launched last Friday to train schools in its use.
"We are also aware schools may have additional audit costs related to the introduction of the new system and we will provide support as appropriate," she said.