The body governing the country's bank-to-bank payment system is trying to find out what has caused late or non-payment of wages or salaries.
The Reserve Bank, which oversees the system, says there was disruption to the transfer system between banks overnight on Tuesday.
Payments NZ chief executive Steve Nicholls says it appears the international payments exchange messaging system Swift had an outage which meant money could not be transferred.
Mr Nicholls says banks are using a back up system to transfer the money and all outstanding payments should be made by early Wednesday afternoon.
He says it is not yet known how many people have been affected.
Mr Nicholls says the problem is different to that which left some employees of government departments and agencies without salary payments on 11 April.
The Banking Industry Association says it was a systems error, not the fault of individual banks.
One of the affected banks, Westpac, says the problem has been resolved and it is working to get the money transferred to people's accounts.