National Australia Bank's chief executive has apologised for an IT glitch that left many customers short of funds while waiting for their latest pay packets.

This morning the bank confirmed that a problem with its IT systems meant many payments made overnight failed to appear in customers' accounts.

The confirmation came when the ABC contacted NAB, after receiving reports this morning from pensioners and Federal Government employees that their regular fortnightly payments had not made it into their accounts.

The problem is not confined to Federal Government payments, with private sector employees also failing to see their pay packets show up.

However, Centrelink and other Federal Government payment recipients made up a large number of those affected, as Wednesday night is a regular government pay-day.

A spokesman for NAB confirmed the problem is at the bank's end, and has resulted in some payments and transactions made overnight being delayed.

The bank says there have also been delays for some NAB EFTPOS, ATM and other electronic banking facilities.

Many NAB customers have complained to the ABC about the lack of communication from the bank to inform them of the issue.

They say the first they heard of the fault was through the news, and are angry they received no warning about the problem from the bank, despite some customers having signed up for SMS updates, or checking NAB's website when they noticed the funds had not arrived.

NAB's chief executive Cameron Clyne apologised to customers for the payment breakdown, after giving a lunchtime speech in Sydney.

"Obviously what's happened today is unfortunate, we're very sorry for the inconvenience it caused customers, we are processing payments now and we're going to work as quickly as possible to fix it," he told reporters.

"Unfortunately in any large organisation these things happen from time to time."

National Australia Bank has also apologised for delays customers experienced on its help line because of the large number of customers ringing its call centres to inquire about the payment problems.

National Australia Bank says that delayed payments and transactions have started to be progressively processed.

The bank says this will take some time due to the large backlog of payments, but hopes to have all of them processed by later today.

NAB says the payments will go through in full once the IT problem is fixed, and adds that customers will not be charged by the bank for slipping into negative balances or failing to make payments because it has already abolished dishonour fees.

However, the bank's statement does not say whether it will compensate customers who are charged late payment fees by third parties due to the payments glitch.