Achilles Macris, former head of CIO International for the bank in London, has been slapped with a £792,900 fine.
The FCA said Macris was responsible for a number of portfolios, including the synthetic credit portfolio, at the time of the trades.
The positions, taken by Bruno Iksil who was nicknamed the London Whale, ultimately led to losses of $5.8bn. JPMorgan Chase was later fined £920m over the scandal.
At the start of 2012, the portfolio started to suffer significant losses - by March it was known that it had made a loss of $200m. Macris had asked for daily risk reports and sought help from outside the division - but failed to alert the watchdog to his concern, "and as a result he failed to meet the standards expected of an approved person," the FCA said.
During a phonecall with the FSA in April of that year, he was aware of the significant issues with the portfolio, but did not raise any concerns or alert the watchdog to the "heightened response" being adopted to address those issues.
"Instead, Mr Macris allowed an inaccurate impression to be given that there had been no material changes since the supervision meeting and that there were not wider causes for concern with the Synthetic Credit Portfolio," the FCA said.
"By failing to inform the authority during the meeting and the call of the causes for concern and by allowing the authority to be reassured concerning the position of the synthetic credit portfolio, the message delivered was not an accurate reflection of the state of the synthetic credit portfolio," it added.
But in a statement, Macris said the outcome represented "a major climb-down by the FCA, after four years that I have spent fighting to clear my name", claiming the regulator had shown "a total disregard for my rights as an individual".
"Having already achieved two significant court victories, in which the FCA was found to have acted against the law in not giving me third party rights, I look forward to further vindication in the Supreme Court, where if I succeed, the FCA will have to expunge from the JP Morgan notice the false and unfair statements made about me," he said.
"The FCA has had several opportunities to admit its mistakes, but instead, at every turn, it has until now sought to defend and justify its position, wasting public funds....
"While I maintain that my efforts in this regard were above and beyond any reasonable standard of transparency with regulators, now that the FCA has accepted that I did not deliberately mislead it, I have decided not to prolong what has been a drawn out and burdensome process and have settled with the FCA, on the basis that there is no prohibition on my working in the regulated sector."
Macris added: "The simple truth is that this has been a costly and ultimately failed investigation which has gone on for far too many years.”