Gunshots were heard at Al-Fateh mosque near Ramses Square in central Cairo, where security forces in riot gear have surrounded pro-Morsi supporters.
State-run MENA news agency reported that gunmen were firing from inside the mosque and live footage on television showed security forces shooting at a minaret from outside.
Scores of protesters, who took those killed and wounded in yesterday's clashes to the mosque, have refused to leave.
Speaking to Al Jazeera by phone from inside the mosque, Omaima Halawa said there were about 700 people, including women and children, inside.
They feared leaving the mosque because "there were thugs outside with the security forces, and that...The security forces were working with the thugs", she said.
Egypt's Nile News reported that about 10 people, mostly women, left the mosque with the body of a woman who died yesterday.
Senior Muslim Brotherhood leader Mohamed Badie's son was among dozens shot dead in the Egyptian capital yesterday.
The Muslim Brotherhood has established a makeshift field hospital in the mosque at Ramses square, the latest flashpoint in a growing crisis.
Two protesters inside the mosque told BBC they did not trust the authorities' promises of a safe exit. They said the protesters had drinking water but there was only one toilet.
Security officials quoted by MENA news agency claimed "armed elements" had opened fire from inside the mosque. They said people were being prevented from leaving the mosque by protesters.
