The violence, worst in a month, came as officials were counting votes in the second phase of the landmark parliamentary elections in the country after the overthrow of longtime President Hosni Mubarak in February.
Social networks showed images of protesters wounded by rubber bullets and stones besides others who were beaten.
The protesters were staging a sit-in in objection to the newly appointed prime minister Kamal Gaanzoury.
Police fired in the air shortly after dawn to try to disperse around 300 demonstrators.
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