Thousands of New Zealanders have missed out on salary payments overnight because of a computer fault.

Payments New Zealand says a network issue on the Swift payments gateway has affected all the banks.

The system is used to transfer files between them, so payment transfers weren't made overnight.

Chief executive Steve Nichols says the fault was discovered early this morning and is being worked on.

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He says some payments have been processed already.

Mr Nichols expects everything to be back to normal soon.