The tape, which was shot last summer in Afghanistan, shows the men urinating on the bodies.
No one has been charged in the case.
Lt. Gen. Joe Waldhauser will name another officer to lead an internal Marine Corps investigation.
That inquiry will be in addition to a criminal probe already under way by the Naval Criminal Investigative Service.
Waldhauser is commander of Marine Corps Forces Central Command, whose area of responsibility includes Afghanistan.
The Associated Press contributed to this report.
