The problem occurred with the Real-Time Gross Settlement payment system, which allows money to be transferred between banks in real time for investment banking and consumer loans.
Even solicitors at the end of the house-buying process are caught up in the problems, although the Bank said some payments will be controlled manually.
The Bank of England said in a statement: “The Bank of England has identified a technical issue related to some routine maintenance of the RTGS payment system and has paused settlement while we resolve it.
“We are working to address this issue as quickly as possible, and restart the RTGS payment system in a controlled manner.
“The most important payments are being made manually and we can reassure the public that all payments made today will be processed.”