Nancy King, global head of commodities, and Jay Rubenstein, head of commodities trading, are leaving after years with the firm, the source said.
The departures were previously reported by Bloomberg and first reported by energy news service SparkSpread.
The move has stoked concerns among some market participants about the use of different communications services in the trade. Commodity trading brokers across the world commonly use messaging services including WhatsApp, WeChat and Intercontinental Exchange (ICE) chat to communicate with traders who put in orders and execute trades.
However, banks, oil majors and commodity merchants have long had strict compliance rules when it comes to communications and several sources have expressed concerns about being monitored by companies when using chat services.
Shell Trading, for example, records and monitors communications, including those by phone, internet messenger, e-mail and other channels, for legal, regulatory and business purposes, where it is legally permissible to do so.
This month, Reuters reported BP terminated four trading and operations staff responsible for Chinese crude oil sales as a result of an internal investigation into trades with Singapore's Hontop Energy.
One of the sources said that a factor behind the terminations at BP was improper use of the WeChat messaging platform as a tool for commercial discussions with counterparties.
Morgan Stanley did not immediately respond to a Reuters request for comment.
The bank did not find any wrongdoing, but the use of those communication channels went against policy, according to the Bloomberg report.
King joined Morgan Stanley as an oil trader in 1986 and was named the sole global head of commodities in June 2016.
Rubenstein joined in 2007 as a power trader and was named global head of commodities trading in June last year, according to his LinkedIn profile.
(Reporting by Devika Krishna Kumar in New York, Niket Nishant in Bengaluru; Editing by Ramakrishnan M., David Gregorio and Sam Holmes)
By Devika Krishna Kumar