The problems were caused by errors in the bank's IT systems which interact and send information about trades to a central system for reporting.
The faults at Barclays Capital emerged during an 11-month period during 2007 and 2008, when the bank made almost 60 million transactions.
Barclays Capital said in a statement, "We have worked constructively and in full cooperation with the FSA throughout the investigation. The regulatory reporting errors were caused by inaccuracies in our data feeds to the FSA. No counterparties, clients, or financial reports were affected in any way."
The FSA said accurate reporting is essential for the watchdog to look out for potential market abuse.
Alexander Justham, FSA director of markets, said, "Complete and accurate transaction reports are an essential component of the FSA's market monitoring work. Barclays' reporting failures could have a damaging impact on our ability to detect and investigate suspected market abuse.
Investment firms must send reports about trades to the FSA at the end of every day. The reports rely on many complex systems linking together. Changes to one system can cause problems for others.
Barclays Capital has fixed the problems.
This article was first published by Computer Weekly.