West Northamptonshire Council says is is 'aware of an issue' after council tax payers logged on to find direct debits had been refunded.
The issue has affected those in the former South Northamptonshire Council district authority area who paid their January 2022 tax instalment automatically.
A council spokesman said: "The payment on January 1 has been debited and then credited back into customers' bank accounts.
"We are investigating this issue with BACS and will provide a further update later."
Tax payers in neighbouring North Northamptonshire were hit by glitches twice in one week after the two new authorities replaced the seven district councils last April.
November's instalment was taken four days early for up to 40,000 households in Wellinborough.
The authority did not reveal how many people were affected although there are thought to be about 40,000 households in Wellingborough.
And, just a few days earlier, council chiefs were forced to issue an apology to hundreds of Corby residents after they each wrongly received a court summons for non-payment of council tax.