The Commodity Futures Trading Commission Thursday fined Morgan Stanley $490,000 for violating rules that require futures brokers to protect clients by keeping their money segregated from other funds on the bank's books.

Morgan Stanley's futures trading unit transferred some $16 million from a segregated client account in 2013, and it also mixed segregated funds and its own money during a six-month period in 2012.

The unit, a so-called Futures Commission Merchant, a U.S. regulatory category that is subject to the CFTC's strict customer protection rules, simultaneously settled the violations with the CFTC.

Client segregation issues were at the heart of two major collapses of futures brokers overseen by the CFTC, MF Global and Peregrine Financial, and the agency has since tightened its rules for the long-regulated industry.

Peregrine founder Russell Wasendorf Sr. begun serving a 50-year jail sentence last year for bilking $215 million from customers, and the CFTC has also charged former MF Global chief Jon Corzine -- a former New Jersey governor and U.S. senator -- for being a key actor in one of the country's 10 biggest bankruptcies.

In the case of MF Global, some $1.6 billion went missing from client accounts, money the firm used to stop gaps in its business as investors quickly lost confidence.

Morgan Stanley said no client money was lost as a result of its issues and that it cooperated fully with the CFTC. It also said it hired an outside auditor to review its procedures and made improvements where required.

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Last year, the CFTC approved rules to better protect customers of futures brokers -- the biggest of whom are units of Wall Street banks -- to tighten up procedures and set aside their own cash to cover client shortfalls.