The deaths Muslim Brotherhood activists were reported in capital Cairo, Alexandria, the Suez Canal city of Ismailia, Fayoum and Minya , Egyptian health ministry said yesterday.
Since Morsi's ouster last year, his supporters have staged near-daily protests calling for his reinstatement, particularly after Friday prayers.
But their numbers have dwindled amid a violent government crackdown.
More than 1,000 people, mostly Islamists, died in street clashes following his overthrow, and thousands have been imprisoned.
Yesterday's protests come as a pro-Morsi National Coalition in Support of Legitimacy, which is spearheading the protest movement, called for demonstrations ahead of the resumption of his trial on Wednesday.
Also Read
And a date for him to be tried on espionage charges has yet to be fixed.
Egypt's military-installed government declared Morsi's Muslim Brotherhood a "terrorist organisation" last month after accusing it of a suicide car bombing at a police headquarters that killed 15 people.
Interior ministry officials have warned that anyone taking part in pro-Brotherhood protests will be punished with five years in jail, while protest leaders might face the death penalty.
The ministry said yesterday it had arrested 120 Brotherhood members nationwide, and said they were armed with explosives, Molotov cocktails, firearms and knives.