At a meeting with heads of 17 brokerages, FSS Gov. Kim Ki-sik said they must conduct reviews of their internal control mechanisms to prevent such errors from happening again.
Kim also urged them to come up with fundamental measures to regain investor confidence, while strengthening ethics rules for employees.
Samsung Securities has been under a firestorm of criticism after it mistakenly paid windfall stocks to its employees as dividends.
The brokerage had originally planned to pay dividends of 1,000 won (US$0.93) to its employees Friday. However, the brokerage mistakenly paid 1,000 shares for each share owned by its workers.
The chaos happened after a Samsung Securities trader made a keyboard entry mistake, typing "shares" instead of "won" in Korean when sending the dividends to employees.
Questions were also raised about whether employees could sell the mistakenly deposited shares, which do not exist, on the stock market and how they could sell the shares without reporting it to the brokerage.
A total of 16 employees at Samsung Securities were found to have sold the stocks Friday morning.
Among them, nine employees sold the stocks even after the brokerage sent a notice about the dividend error, according to the securities firm.
Samsung Securities said it relieved 20 employees, including the 16 who sold the stocks, from duties and will hold them accountable for the dividend chaos.