Kiwibank says 99 per cent of faulty transactions made yesterday during a Visa Debit Card glitch have now been reversed.

Customers should have the correct balance showing in their accounts, a spokeswoman for Kiwibank told the Herald.

Between 1pm and 2.30pm yesterday, some customers were charged multiple times for purchases after their card was declined.

"Some customers, because they were getting a declined message when doing the payment, did it multiple times," Kara Tait, external communications manager for Kiwibank, said.

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"It was resolved quite quickly. It was only an issue for an hour and a half this afternoon, but obviously it did have an impact on our customers."

Kiwibank said the issue affected only 2 per cent of its Visa Debit Card customers.

The technical team is urgently working to resolve the final five outstanding transactions.

"We know this has had a customer impact and we really apologise for the inconvenience to people and we'll do the right thing by our customers when we've got a solution sorted," Tait said.