The bank must make the payment to the Department of Justice after it failed to detect millions of dollars of drug money being transferred into several accounts under its control.
BankAtlantic admitted that it had made errors in failing to maintain an adequate anti-money laundering system, with chief executive Alan B. Levan saying that the bank has taken great steps to rectify the problems.
"We identified deficiencies in out anti-money laundering compliance in 2004," he said.
"Since that time we have worked tirelessly to ensure that we are in full compliance with the Bank Secrecy Act and other anti-money laundering laws and regulations, and have made significant investments in personnel and compliance systems."
Under the Bank Secrecy Act, US banks are required to establish and maintain an anti-money laundering system, enabling them to report suspicious financial transactions to the relevant authorities.
Alice S. Fisher, assistant attorney general of the criminal division of the treasury department, said that it was important that banks' obligations concerning anti-money laundering were not ignored.
"Banks that fail to adequately know their customers and screen their transactions for suspicious activities can be exploited by the international drug cartels, professional money launderers, terrorists and other criminals," she said.