UPDATED 8.40AM Holiday pay errors have cost workers more than $2 billion, according to the official workplace regulator.

And Government departments are amongst the worst offenders.

SEE ALSO: Dozens of major employers facing payroll problems

Labour Inspectorate documents name the Police and the Ministry of Business and Innovation among the organisations which have had to make good payments to 26,000 workers.

In total, at least $35 million has been paid out by 25 companies and agencies.

CTU President Richard Wagstaff said New Zealand Post, Fairfax, Fonterra, The Warehouse, Auckland Council and the Ministry of Social Development are still being investigated.

Mr Wagstaff said a probe of holiday pay issues which began earlier this year has uncovered flaws in payroll software.

"MBIE itself said that it could be that the failure of payroll providers to comply with the law for years has left hundreds of thousands of New Zealanders out of pocket by up to $2 billion," he said.

"We're not suggesting anyone's deliberately under-changing their staff - it seems to us it's probably a software problem, and organisations just not paying due attention to insuring people are paid properly.

"The Ministry of Business, Innovation and Employment itself is one agency itself that's had a problem with its payroll, ironically perhaps. But it shows that its entirely possible for it to occur to any organisation."