Waving Egyptian flags and holding up pictures of Morsi, marching protesters chanted slogans against the move by army chief Abdel-Fatah el-Sissi.
Morsi's Muslim Brotherhood mobilised the marches under the banner, "Breaking the Coup."
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At least 400 protesters marched through northern Sinai Peninsula's main city of el-Arish. The military dropped flyers urging people to act protect their land and Sinai from "terrorists."
The lawless part of northern Sinai has been the scene of attacks by Islamist militants against Egyptian security forces and police for two years. The pace of the violence has picked up since Morsi's overthrow.
To combat the wave, Egypt has beefed up its forces there with the agreement of neighbouring Israel, which is also concerned about the growing strength of militants there.
Despite sweltering heat, pro-Morsi supporters also took to the streets in the northern coastal city of Alexandria and several Nile Delta cities.
Today's rallies coincide with the 10th day of the Muslim holy month of Ramadan, which Egyptians celebrate as the day their armed forces crossed the Suez Canal in the 1973 war with Israel. Fighter jets flew overhead in Cairo to mark the day with an air show.
Youth activists who launched the mass protests that led to Morsi's ouster by the military are planning a demonstration in Cairo's Tahrir Square to also mark the 10th day of Ramadan, raising fears of clashes in the capital.
Though the two main protest sites will be several kilometres apart in the city of 18 million, marches by either side could spark violence.
About 60 people have been killed in clashes with security and local residents that erupted out of demonstrations since Morsi's ouster. Most of them were killed in a single clash outside a Republican Guard base in Cairo between Brotherhood supporters and the military.
The military replaced Morsi with interim President Adly Mansour, who pledged yesterday in a pre-recorded televised message to protect his country against those who seek chaos and violence in the aftermath of Morsi's toppling.
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