The officer, Col. Sayad Khodayee, was deputy commander of a covert unit tasked to murder targeted people in various countries, the report said on Wednesday, citing the Israeli officials.
Khodayee, 50, was killed on Sunday near his home in Tehran when two gunmen approached his car and fired five bullets, the report said.
The Iranian government accused Israel for Khodayee's killing and the country's National Security Council promised a harsh response.
The Israeli officials reassured the US government that by eliminating Khodayee they sent a message to Iran to stop the activities of the covert group within the Quds Force known as Unit 840, the report said.
Israel claims Khodayee was allegedly responsible for operations in the Middle East near Iran and against civilians and officials from Europe, the United States, Kenya, Ethiopia and the United Arab Emirates.