The Muslim Brotherhood says its members were staging a pro-Morsi sit-in at the site they believe ousted President Mohammed Morsi is being held.
It called the killings "a massacre".
The army's account is different. They said a terrorist group had tried to storm the barracks.
Mr Morsi was removed by the army last week, arrested, and replaced by Adli Mansour, the top judge of the country's Constitutional Court, who is now serving as an "interim leader".
Army chief Gen Abdul Fattah al-Sisi said Mr Morsi had "failed to meet the demands of the people".
Mr Mansour, an interim council and a technocratic government have been put in place until new presidential and parliamentary elections are held – although no timetable has been set.
Mr Morsi is an Islamist and Egypt's first freely elected leader. He described the Army's actions as a military coup.
Supporters are demanding his reinstatement.
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