A spokesman for the Co-operative said the error occurred on Tuesday.
He was unable to say how many people were affected but it is thought that it could run into hundreds of thousands.
Those affected will have their money credited directly back to their accounts within the next 24 hours, he said.
The Co-operative has also promised to reimburse people who have incurred charges as a result of the error, such as overdraft fees.
A spokesman for the Co-op said the mistake was down to a “processing error”