Mohamed al-Shafie had been missing since Jan. 29 and his mother discovered his body at a Cairo morgue Sunday, al-Masry al-Youm reported.
An autopsy ordered after the mother filed a police report found a birdshot wound to al-Shafie's head, the report said Monday.
In her complaint, the mother said her son had been tortured before he was killed.
Al-Shafie was the second activist to disappear since protests marking the second anniversary of Egypt's 2011 uprising.
Mohamed al-Gendy disappeared Jan. 28 and died shortly after he was found in critical condition in a hospital.
Activists said al-Gendy had been tortured at a police camp but police said he was in an auto accident.