Pentagon spokesman Sean Parnell confirmed Thursday that McGee retired earlier this month, The Hill reported.
"Gen. McGee is retiring, and the War Department is grateful for his service," Parnell said in a statement. "Lt. Gen. JP McGee will retire after nearly three years of outstanding leadership and service on the Joint Staff."
"We are grateful for his 35 years of honorable and dedicated service to the nation," a Joint Chiefs spokesperson told CNN. "We owe him a great debt for his service, and it is regrettable [that] anonymous sources would put the focus anywhere else."
CNN cited unnamed sources as saying McGee was targeted for removal starting in the spring due to his close working relationship with former Defense Secretary Lloyd Austin and Joint Chiefs Chairman Gen. Mark Milley.
McGee differed with Hegseth and Caine on several issues, including the military strikes on alleged drug smugglers in the Caribbean Sea and Pacific Ocean over the past two months, as well as the war in Ukraine, according to CNN.
Parnell denied McGee retired due to differences with Hegseth and Caine.
The general served on the Joint Chiefs of Staff as its director for strategy, plans and policy, and former President Joe Biden nominated him to become director about a year ago.
The Senate did not confirm McGee's promotion, and the administration did not nominate him after President Donald Trump replaced Biden in January.
While on the Joint Chiefs of Staff, McGee advised Caine regarding long-term strategy, weighing the risks of possible military actions and contingency plans.
McGee's departure is one of more than a dozen among senior military leaders since Trump was inaugurated for his second term in January.
Hegseth ordered the nation's highest-ranking military officers to attend a meeting at the U.S. Marine Corps Base in Quantico, Va., on Sept. 30.
Many who attended the meeting viewed it as a "'loyalty test'" in which Hegseth urged them to "be killers for America," Military.com reported.
Parnell downplayed criticism of the meeting and said Hegseth announced that "promotions and combat assignments will be given based on merit and ability, not diversity quotas."
"These core principles have been the foundation of our force for generations and drive our entire institution," he told Military.com.
McGee's 35 years of service included 10 deployments to support combat operations in Iraq and Afghanistan and many staff tours, according to the Joint Chiefs of Staff.
He also was the commanding officer of the U.S. Army's 82nd Airborne Division, 75th Ranger Regiment and the 101st Airborne Division.
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