The Brotherhood, which demands the reinstatement of ousted president Mohamed Morsi, has organised near-daily protests despite its designation last month as a terrorist organisation.
Yesterday's violence was the deadliest in almost three months, after Morsi supporters rallied in the thousands in defiance of the interim government's designation of the Brotherhood as a terrorist group last month.
The designation carries harsh prison sentences for members arrested during demonstrations or leaders of the influential Islamist movement.
The state "will confront the activities of this terrorist group with full force," it said.
Police arrested 258 suspected protesters during the clashes, security officials said.
The crackdown prompted another diplomatic row between Egypt and Qatar, which had supported Morsi and criticised on yesterday's Cairo's treatment of the Brotherhood and protesters.
The Egyptian foreign ministry said Saturday it summoned Qatar's ambassador in Cairo in protest at Doha's criticisms, and to object to Qatari broadcaster Al-Jazeera's coverage of the unrest.
The decision was "a precursor to a shoot-to-kill policy against demonstrators," said a foreign ministry statement, published by the official Qatari QNA news agency.
More than 1,000 people, mostly Islamists, have been killed in street clashes, and thousands have been imprisoned, in the crackdown on Morsi's supporters following his ouster.
The military is also battling an Islamist militant campaign in the Sinai peninsula that has killed scores of soldiers and policemen since Morsi's overthrow in July.
Another soldier was killed today when a road side bomb detonated near his vehicle, the military said.
