Accurate and timely reporting of transactions was crucial for spotting insider trading and market manipulation, the FCA said.
The record fine for reporting failures reflected the severity of the misconduct and a failure to adequately address the root causes over several years despite substantial guidance from the regulator and a poor history of transaction reporting compliance, it added.
The fine follows a private warning to the bank in 2002 and a fine of 150,000 pounds in 2006.
"Proper transaction reporting really matters. Merrill Lynch International has failed to get this right again, despite a private warning, a previous fine, and extensive FCA guidance and enforcement action in this area," said Georgina Philippou, acting head of enforcement at the FCA.
Read MoreWatchdogs impose $3.4B fines in bank forex probe
"The size of the fine sends a clear message that we expect to be heard and understood across the industry."
Bank of America Merrill Lynch had no immediate comment.
The FCA said the fine equated to 1.5 pounds per incorrect or non-reported data for the first time, up from a pound per line in the three most recent transaction reporting cases because those fines have not been high enough to achieve "credible deterrence".
The watchdog has, to date, fined 11 other firms for transaction reporting breaches: Deutsche Bank, Barclays, Credit Suisse, Instinet, Getco, Commerzbank, Societe Generale, City Index, James Sharp & Co, Plus500UK, and Royal Bank of Scotland.