Numerous staff at Fairfax Media are being underpaid after the firm got a company in India to run its pay system.
It is affecting workers who produce Stuff.co.nz and newspapers including the Dominion Post and The Press.
They have dubbed the system 'NovoFax', in reference to the flawed school pay system Novopay, and some staff have been short-changed hundreds of dollars.
RNZ has been told the old payroll system, owned by a New Zealand and Australian company, worked well, but was replaced with a new system which caused problems of "epic proportions".
The first pay staff received via the new Employee Self-Service (ESS) was in November and there have been at least four or five pay cycles since then.
RNZ has been told there were problems from the outset, with people consistently paid incorrectly. Some people's pay packets were only out by a few dollars, some $200 to $300 out, and, in some cases, payments were up to $900 short.
Those who were paid monthly escaped being underpaid but those paid fortnightly were affected.
The ESS payroll model put the onus on staff to do their own timesheets and they needed to check that their rosters matched their timesheets.
However, management had only had limited training in what they were supposed to do and often did not sign off for overtime when they were supposed to.
RNZ was also told annual leave allocations were all over the place and changed week to week.
While those had been mostly fixed, it had occurred around Christmas and New Year when people were taking more leave, making it hard to work out if they had lost work entitlements.
When pay was topped up, it was taxed at a higher rate.
When staff phoned the ESS call centre in India with complaints, the language barrier meant they frequently could not understand what was being said.
Staff also often did not get a reply to emails.
Sources said the system was hyped as being all about workers being given more control over their pay, but it was seen as a cost-cutting mechanisam.
They said they were feeling frustrated and would like to see the old system reinstated - but did not see an end to the problem.
Union and management respond
Union E Tū confirmed there were numerous issues every pay cycle.
Its spokesperson, Paul Tolich, said it was aware of the situation and, sometimes more than once a week, the union was asking Fairfax management to fix issues as they came up.
The union had been getting the problems sorted on a case-by-case basis since the pay system came into effect, he said.
A member of Fairfax management confirmed there had been issues with the new system but, despite that, Fairfax Media denied there was a problem.
The company said there was no-one available to be interviewed on Tuesday night but said in a statement: "We introduced a new payroll system - ESS - last year. We worked through some queries and issues at go-live, but these were addressed."