Staff at Fairfax Media have been short-changed up to $900 after the firm outsourced its pay system to a company in India.
It is affecting fortnightly-paid workers who produce Stuff.co.nz and newspapers including the Dominion Post and The Press, Radio New Zealand has reported.
RNZ was 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 from the outset people were regularly paid incorrectly.
The new system requires staff to do their own timesheets and check their hours match their pay. This extra responsibility has been made difficult by management lacking training and neglecting to approve overtime.
The major problem initially was incorrect annual leave allocations around the Christmas and New Year holiday period.
Sources told RNZ the system was hyped as being all about workers being given more control over their pay, but it was seen as a cost-cutting mechanism.
Union E Tū spokesperson Paul Tolich said sometimes more than once a week, the union was asking Fairfax management to fix issues as they came up.
Fairfax management denied there was a problem but confirmed there had been some teething issues.
In a statement Fairfax Media said: "We introduced a new payroll system - ESS - last year. We worked through some queries and issues at go-live, but these were addressed".