The Ministry of Education's plan to cut staff in its payroll unit shows the government has lost control of it, Labour says.

Association Education Minister Craig Foss was utterly flabbergasted when he found out about it and thinks the unit needs more resources as it deals with the teacher pay crisis, Fairfax reports.

"Any plan to cut payroll staff numbers is totally out of sync with what the ministry is trying to achieve with the Novopay rollout," he said.

Some school staff haven't been paid for months because of Novopay's error-ridden system and it failed to meet the government's deadline of Wednesday this week to fix the problems.

Public Service Association national secretary Brenda Pilott says the ministry intends cutting the number of positions in the payroll unit from 23 to 14 when the Novopay system is working properly.

Labour's state services spokesman, Chris Hipkins, says the fact that Mr Foss was flabbergasted shows the government isn't in control of the ministry.

"It simply defies belief that the ministry would begin a restructure involving the very staff tasked with fixing the mess," Mr Hipkins said on Friday.

"And those waiting for their pay will rightly be outraged when they learn the minister in charge doesn't seem to know anything about it."

Mr Hipkins says Mr Foss signed off on the implementation of the Novopay system and then lost control of the debacle that followed.