The Pentagon said Commander Job Price, 42, did not die in combat, and that his death is under investigation.
Price, of Pottstown, Pennsylvania, died Saturday of a "non-combat related injury while supporting stability operations in (central) Uruzgan province, Afghanistan," a Defense Department statement said.
It said Price was assigned to a Naval Special Warfare unit in Virginia Beach, Virginia.
CNN and NBC News reported that Price commanded SEAL Team 4, one of eight SEAL team deployments.
The family has been notified of the death, which is being investigated as an apparent suicide, a US military official with direct knowledge of the event told CNN.
The official said there was no immediate indication that Price was involved in any military-related investigations or controversies.
CNN reported that military staff found Price`s body with an apparent gunshot wound.
It said the Navy SEAL commander oversaw more than two dozen commandos and support staff conducting counterterrorism operations in insurgent-heavy Uruzgan.
SEAL Team 6 became famous after tracking down and killing Al-Qaeda leader Osama bin Laden, who is accused of being the architect of the September 11, 2001 attacks on the United States.
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