According to the report, Mr al-Masri’s daughter - Osama bin Laden’s widowed daughter-in-law - was also targeted.
The CIA and Israeli Prime Minister Benjamin Netanyahu declined to comment when approached by the Associated Press.
Iran’s foreign ministry denied the report, according to the New York Times, which first reported the operation.
Mr al-Masri remains on the US’s most wanted terrorist list, with the country’s department of state offering a reward of up to $10 million (£7.5m) for information.
He was accused of helping to plan attacks on US embassies in Tanzania and Kenya in 1998. The operation to kill him reportedly took place on the anniversary of the bombings.
