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All payments to and from the Nationwide Building Society to other building societies and banks are delayed.
It says direct debits and standing orders are working normally. Money can still be moved between Nationwide accounts, it added.
In a statement on its website it said it was "sorry for any problems this may cause."
"We're working to get things back to normal as quickly as we can", the statement continued.
Nationwide says customers can continue to use their cards online and in shops, log-in to their banking apps, and withdraw money at cash machines.
The BBC is receiving reports of the impact the problems are having - one customer says he is unable to redeem his mortgage because of the issue.