He said 41 teaching or support staff had received advances and 23 had indicated they were willing to wait to be paid in the next fortnightly pay cycle.
When questioned by Ms Mahuta on the total amount of outstanding pay, Mr Foss said that information was not available under the Novopay system.
"Every non-payment or under-payment brought to the attention of the ministry if being addressed," he said.
Mr Foss would not say how long it would take for the problems with the system to be resolved.
Secretary for Education Lesley Longstone said extra staff were working at the Novopay call centre and on data entry.
Novopay experts were also visiting schools to assist principals and payroll administrators.
"Specialist training sessions will be offered for all schools to assist with end-of-year pay-cycle processes," she said.
"The Novopay system is paying the vast majority of staff correctly, However, the ministry acknowledges there are issues that must be addressed."
A survey by the New Zealand Principal's Federation found around 90 per cent of principals had unresolved problems with the last pay cycle.
Half of the 2400 principals contacted responded to the survey.
It found 86 per cent did not have confidence the problems would be resolved by the end of the year.