Once hackers gain access to a financial institution's system, often through phishing, they'll alter account balances as well as disable maximum ATM withdrawal amounts and transaction limits. That way, they can quickly take out large amounts of cash from ATMs with fraudulent bank cards made from stolen card data and gift cards.

Last month, Krebs on Security reported on two successful applications of this type of scheme. Hackers were able to steal around $2.4 million from The National Bank of Blacksburg through two ATM cash-outs in 2016 and 2017.

As part of the warning, the FBI is encouraging banks to institute more rigorous security measures such as stronger password requirements, two-factor authentication and more network monitoring.