Under several pseudonyms, including Abu Muhammad al Masri, the Egyptian-born activist had long been on the FBI’s list of “most wanted terrorists”.
He was shot dead by two men on motorcycles in the streets of Tehran on August 7, at the behest of the United States, according to the New York Times.
Masri was reportedly killed along with his daughter, Miriam, the widow of Osama bin Laden’s son, Hamza bin Laden.
The paper says IranState news media identified the victims as Habib Daoud, a Lebanese history teacher, and his 27-year-old daughter Maryam – however, it is claimed that these names were merely a pseudonym.
Masri was accused of helping to organize the bombings of several American embassies in Africa in 1998.
Almost simultaneous attacks in Nairobi, Kenya, and Dar es Salaam, Tanzania, left 224 dead and more than 4,500 injured.
An FBI poster, describing Masri as around 58, with a scar on the right side of his lower lip and a possible mustache – offered up to $ 10million (£ 7.6) for information leading to his capture.
Masri was a professional football player in the Egyptian Premier League in his youth, according to official documents previously filed in lawsuits in the United States.
In the late 1990s, he was said to have been one of bin Laden’s closest associates.
Bin Laden was the leader of Al Qaeda at the time of the September 11, 2001 attacks and was killed in an American raid on Pakistan ten years later.
The newspaper cited intelligence officials as the source of Masri’s death, but Israel, America and Al-Qaeda have yet to publicly acknowledge the murder.
Iran on Saturday denied the report, saying there were no Al Qaeda “terrorists” on its soil.
Foreign Ministry spokesman Saeed Khatibzadeh accused the United States and Israel of “linking Iran to such groups by lying and divulging false information” in an attempt “to evade responsibility for the criminal activities of this group and other terrorist groups in the region ”.
He called it the “Hollywood script” trap of senior US and Israeli officials, and warned the media not to believe it.
In October, an Afghan security source told Reuters that Masri was killed in the Pasdaran area of Tehran, but Reuters had not been able to corroborate this information.
The Times said U.S. authorities have been following Masri and other Al Qaeda operatives in Iran for years.
Israel has previously said its intelligence services entered Iran, including claiming in 2018 that it smuggled suspected archives of Iranian nuclear secrets.
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Masri had lived in Tehran since 2015, officials told The Times.
Iran and Al Qaeda have always been enemies because of the Sunni-Shiite divide.
According to the Times, unnamed U.S. intelligence officials have said Iran may have let Masri live freely in the country to conduct operations against their common adversary, America.
Despite the loss of several top leaders over the past decades, Al Qaeda has maintained active affiliates from the Middle East to Afghanistan to West Africa.
In the past month, two more Senior al-Qaeda leaders killed in Afghanistan by local security forces.