Citing government sources, NBC News reported Mohammed al-Zawahiri, brother of al-Qaida leader Ayman al-Zawahiri was arrested at a checkpoint in Giza. Mohammed al-Zawahiri is a supporter of the Muslim Brotherhood and a more extreme faction in Egypt, Al Gama'a Al Islamiya.
Security forces fired at the minaret of the al-Fatah mosque during the standoff, saying snipers were using it, CNN reported. Protesters inside resisted calls to surrender for hours, fearing they would be attacked as they left.
The mosque became the focus of the struggle in Cairo after more than 600 people were reported killed in violent clashes between police and demonstrators protesting Morsi's overthrow. CNN said footage from inside the mosque showed many protesters under arrest.
The official Middle East News Agency said hundreds of Morsi supporters left the mosque in central Cairo where they had been holed up overnight.
Most of the protesters, primarily supporters of the Muslim Brotherhood, left peacefully but some holdouts were routed by security troops who fired tear gas into the building and then made a forced entry. A witness told the Los Angeles Times one woman in the mosque suffocated in the gas attack.
Opposition leaders had called on crowds of protesters to converge on the mosque to support the people inside, but police managed to prevent anyone from entering the building.
Outside, there were charges and counter-charges about who was responsible for the standoff and the overall violence that has killed around 173 people since Friday.
CNN said a presidential adviser expressed the interim government's condolences for the rising casualties, but laid the blame for the trouble on outsiders and called on the pro-Morsi protesters to "come to their senses."
"We are not facing a political struggle," said Mustapha Higazi . "We are facing war waged by extreme forces."