Ministry of Business, Innovation and Employment is facing a major problem in its payroll system that may affect up to 3000 employees.

MBIE Minister Steven Joyce said the issue involved how holiday entitlements and shift pay were calculated. It could potentially involve millions of dollars but ministry chief executive David Smol had told him it would involve only small amounts in individual cases, though Joyce could not put a dollar figure on those.

The system was installed more than 10 years ago at the Department of Labour but was used for the merged super-ministry MBIE.

It is a potential embarrassment for Joyce who was called in to fix the much bigger Novopay education payroll system in 2014 that was beset by problems since it was installed in 2012.

But Joyce said it was not on that scale.

Issues had first come to light in 2012, involving the Immigration department payroll, but they were resolved.

The latest problems were being “scoped” and he had first been informed of the problem some weeks ago.

“It’s disappointing, but around an area that’s fiendishly difficult, and that’s not to excuse it,” he said.

The providers of the system were working to fix the problem as quickly as they could, though that could be “weeks to months away”.

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