Sheikh Akram, the imam of the Ali Ibn Abi Taleb (AS) Mosque, was killed on Thursday in the Ajamy area of the northern city.
Egyptian officials accused him of promoting anti-government sentiments in his sermons.
Sheikh Akram’s family says security forces threw him off the balcony of his house, but security forces claim he fell while trying to escape arrest.
Meanwhile, security sources in the northern part of the city killed a protester during a demonstration against the military-appointed government.
Egypt has been experiencing unrelenting violence since last July when the army ousted Egypt’s first democratically elected President Mohamed Morsi, suspended the constitution, and dissolved the parliament. It also appointed the head of the Supreme Constitutional Court, Adly Mahmoud Mansour, as the new interim president.
The interim government has launched a bloody crackdown on Morsi’s supporters and arrested thousands of Muslim Brotherhood members, including the party’s senior leaders.
Egyptian universities have also been the scene of violent clashes, with students calling for the reinstatement of Morsi and demanding an end to the crackdown on Brotherhood supporters.
On December 25, the military-appointed government listed the movement as a “terrorist” organization over alleged involvement in a deadly bombing, without investigating or providing any evidence.
Earlier this month, Amnesty International criticized Egyptian authorities for using an “unprecedented scale” of violence against protesters and dealing “a series of damaging blows to human rights.”
According to the UK-based rights group, 1,400 people have been killed in the political violence since Morsi’s ouster, "most of them due to excessive force used by security forces."