A new payroll system is being blamed for hundreds of employees of the contracting company Spotless being left out of pocket.
Workers' union E Tū described the situation of some workers, who were owed hours worth of pay, as a 'nightmare'.
But the company, which has over 5000 staff working as cleaners and hospital kitchens staff in New Zealand, said the majority of the problems had been resolved.
One affected cleaner, whose contract prohibits him from speaking to the media, said he now owed more than $300 to Housing New Zealand and was having to borrow money to feed his young family.
"My kids are suffering. Last week, I couldn't pay for milk powder for my four-month-old," he said.
"I was told, 'go to WINZ, they'll help.' But I don't need WINZ. I need to be paid."
Jill Ovens, an industry co-ordinator at E Tū, said pay issues were systemic among cleaning contractors, but it got worse after a new payroll system was introduced at Spotless before Christmas last year.
One example was the Mangere's Southern Cross school campus, where seven cleaners claimed pay arrears in February of about 300 hours work, she said.
Ms Oven said there were also problems with the voice recognition software used by workers to clock on and off.
"It doesn't seem to recognise Pacific Island voices or if someone has a cold, and when that happens, people can't get into the payroll system to be paid."
A spokesperson for Spotless acknowledged there had been "short-term discrepancies" in payments, as a result of the new payroll system.
"We have proactively managed this transition, and are confident that the majority of issues have been resolved."
She said the voice recognition software worked with all cultures and languages, "noting that errors are usually linked to training, rather than system failures".
This is not the first time Spotless has made headlines.
In 2007 more than 800 workers were locked out for almost two weeks following a breakdown in negotiations over a pay dispute.
In 2015, it emerged nine of their contractors working in Parliament were employed on zero-hours contracts.
The company agreed to end all zero-hours contracts in May 2015.
About 1000 Spotless workers are members of the E Tū union.