A total of 1,079 "rioters" were arrested across Egypt on the third anniversary of the January 25 revolution, the interior ministry announced in a statement late on Saturday.
Security forces said it had prevented "the Muslim Brotherhood's terrorist plot to disrupt celebrations" by "attempting to block roads, chant hostile slogans and provoke riots."
Some of those arrested were accused of possessing Molotov cocktails and fireworks, live ammunition and birdshot rifles.
The fiercest clashes, according to the statement, took place in Alf Maskan and Al-Matarya districts of Ain Shams in east Cairo, where Brotherhood supporters allegedly fired birdshot.
Several police officers were injured in the clashes.
According to the health ministry at least 29 civilians were killed on Saturday as violence erupted in Cairo, Giza, Upper Egypt's Minya governorate, Alexandria and other cities.
In addition to Brotherhood loyalists, police also clashed with anti-Brotherhood and anti-military protesters.