Supreme Leader Mojtaba Khamenei is reportedly still playing a critical role in Iran’s war strategy marking the strongest indicator of his influence over Tehran since rising to power — and the first to come from US intelligence sources.

Khamenei, 56, is believed to be directing Iran’s negotiations with the US from his unknown hideout, multiple sources familiar with US intelligence reports about him told CNN, despite being badly disfigured and having lost a leg during the US and Israeli strikes that started the war.  

The new supreme leader was previously described as still “mentally sharp” by people close to his inner circle, who said he was meeting with senior Islamic Republic officials and helping to make decisions on the Pakistani-mediated peace talks.

Khamenei — who US intel believes is “probably gay,” despite leading a nation where homosexuality is outlawed — has yet to be seen or heard since he was appointed as his father’s successor in March.

State media has read written statements attributed to the younger Khamenei on just three occasions since taking over theocratic regime.

Iran, however, claims its new ayatollah is in good physical shape, despite the damning reports.

Khamenei “is now in complete health,” Mazaher Hosseini, head of protocol in the office of Iran’s supreme leader, said Friday.

“Thank God, he is in good health,” Hosseini told an Iranian crowd.

“The enemy is spreading all kinds of rumors and false claims. … He will speak to you when the time is right.”

Hosseini claimed “a small piece of shrapnel had hit him behind the ear,” but assured Khamenei was on the mend. The ayatollah, however, is believed to have bad burns on his face, arm, torso and leg on one side of his body, according to the same intelligence sources.

The cleric also isn’t using any electronics, making it harder for foreign intelligence to track Khamenei’s whereabouts. He is reportedly only interacting with senior leaders face to face or by sending messages via a courier.

Even though his influence over the negotiations to end the war and reopen the Strait of Hormuz has been felt, senior Islamic Revolutionary Guard Corps officials are believed to be running the day-to-day operations inside Tehran. 

Iran’s president, Masoud Pezeshkian, claimed Thursday he recently met with Khamenei for more than two hours — marking the first reported in-person meeting with the Islamic Republic ruler.

“What struck me most during this meeting was the vision and the humble and sincere approach of the supreme leader of the Islamic Revolution,” Pezeshkian gushed, according to Iranian state media.