The body of Mojtaba Ahmadi, who served as commander of the Cyber War Headquarters, was found in a wooded area near the town of Karaj, northwest of the capital Tehran.
Iranian police said two people on a motorcycle had been involved in the killing of Ahmadi.
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Ahmadi was last seen leaving his home for work on Saturday and he was found with two bullets in the heart, British daily The Telegraph reported while quoting Alborz, a website linked to the Revolutionary Guard Corps.
"I could see two bullet wounds on his body and the extent of his injuries indicated that he had been assassinated from a close range with a pistol," a witness was quoted as saying by the website.
In a statement, the Imam Hassan Mojtaba division of the Revolutionary Guard Corps said Ahmadi's death was being investigated. It warned against speculating "prematurely about the identity of those responsible for the killing".
According to The Telegraph, Western officials said the information was still being assessed, but previous deaths have been serious blows to Iran's security forces. The death of Ahmadi could be an extension of this campaign of subterfuge.
Iran has been accused of carrying out a number of cyber attacks detected in the West.
Shashank Joshi, an expert at the Royal United Services Institute (Rusi), said this was seen as a lesser threat than the nuclear programme.
"Iran's cyber attacks on Israel and elsewhere in the region are a rising threat and a growing threat, but it hasn't yet been seen as a major and sustained onslaught, so it would be pretty novel and significant to take this step in the field of cyber-warfare at this time," Joshi said.
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