One person was jailed for life, three people to 15 years and 45 others to five years, a military statement said.
The defendants were accused of opening fire at soldiers during riots in the port city of Suez last month.
The riots followed a deadly crackdown by security forces on two pro-Morsi protest camps in the capital, Cairo.
Hundreds of people, mostly members of Mr Morsi’s Muslim Brotherhood, were killed when the sit-ins outside the Rabaa al-Adawiya mosque and at Nahda Square were cleared on 14 August.
The unrest in Suez, 140km (87 miles) to the east of Cairo, on 14 and 16 August left more than 30 dead.
It is not clear if those convicted on Tuesday are Brotherhood members. But if they are, the verdicts would be the first affecting the Islamist group since the military launched a campaign against it after ousting Mr Morsi.
Earlier, military sources said 11 Morsi supporters had got life sentences.
‘Internal and external forces’
State prosecutors announced on 1 September that after almost two months in detention at a secret location, Mr Morsi would stand trial for inciting murder and violence.
The charges relate to the deaths of at least seven people during clashes between opposition protesters and Brotherhood supporters outside the Ittihadiya presidential palace in Cairo in December 2012.
Fourteen other senior Brotherhood figures, including Mohammed al-Beltagi and Essam al-Erian, will be tried on the same charge.
The group’s general guide, Mohammed Badie, has also been arrested.
Also on Tuesday, a court in Cairo ordered the closure of four television stations, including the Brotherhood’s Ahrar 25 TV and al-Jazeera’s Egyptian affiliate Mubasher Misr, saying they were operating illegally.
The stations were seen by the authorities as being sympathetic to the Brotherhood.
In the evening, thousands of supporters of Mr Morsi took to the streets in towns and cities across Egypt to denounce the military-backed interim government.
The marches in the capital, the Nile Delta, Upper Egypt and along the Suez Canal were held under the slogan “The coup is terrorism”, a reference to the government’s portrayal of its crackdown on the Brotherhood as a fight against terrorism.
Hundreds of people in Nasr City, an eastern suburb of Cairo, chanted “the revolution will continue” and “down with military rule”, according to the Reuters news agency.
Interim President Adly Mansour warned that “internal and external forces” would “spare no effort to block the implementation” of his transition plan, which envisages an amended constitution to be put to a referendum within months and parliamentary elections to be held by early 2014.
“We have seen the violent incidents witnessed by the country. In their own words, they are trying to paralyse Egypt,” he told state-run Nile News.
“The state, with all its agencies, will not allow any party to stand before satisfying the aspirations of the people,” he added.