The deaths of the prisoners, captured during the fierce fighting in recent days around Cairo's Ramses Square, came as Gen. Abdel-Fatah el-Sissi also called for the inclusion of Islamists in the government. Meanwhile, security forces detained Muslim Brotherhood members in raids aimed at stopping more planned rallies supporting ousted President Mohammed Morsi - which the military-backed government says fuels the violent unrest.
The suspects killed were part of a prison truck convoy of some 600 detainees heading to Abu Zaabal prison in northern Egypt, security officials told The Associated Press. Detainees in one of the trucks rioted and managed to capture a police officer inside, the officials said,
Security forces fired tear gas into the truck in hopes of freeing the badly beaten officer, the officials said. The officials said those killed died from suffocating on the gas.
The officials spoke on condition of anonymity because they were not authorized to speak to journalists.
However, the officials' version of event contradicted reports about the incident carried by state media. The official website of Egyptian state television reported that the deaths took place after security forces clashed with militants near the prison and detainees came under fire while trying to escape. The official MENA state news agency also said the trucks came under attack from gunmen.
State media also said all those killed and the gunmen belonged to the Muslim Brotherhood, the organization that Morsi hails from. The officials who spoke to AP said some of the detainees belonged to the Brotherhood, while others didn't.
The differences in the accounts could not be immediately reconciled Sunday night.
The violence adds to the ever-rising death toll in days of unrest. On Saturday alone, clashes between Morsi supporters and police killed 79 people, according to a government tally released Sunday and carried by MENA. That raised the death toll for four days of unrest across the country to nearly 900 people killed. Some 70 police officers were killed in clashes with protesters or retaliatory attacks during the same period, according to the Interior Ministry.
The clashes began Wednesday when security forces dismantled two encampments in Cairo of Morsi supporters, who demanded his reinstatement. The military overthrew Morsi in a bloodless July 3 coup after millions took to the street demanding him to step down.
Egypt's military-backed interim government declared a state of emergency after Wednesday's clashes and imposed a curfew, turning the capital into a ghost town after 7 p.m. every night. The government also began taking harsher measures to crippling the Brotherhood.
Security forces arrested hundreds of Muslim Brotherhood members early Sunday morning in raids on their homes in different cities, aimed at disrupting planned rallies to support Morsi. The Cabinet also held an emergency meeting to discuss potentially banning the group, a long-outlawed organization that swept to power in the country's first democratic elections a year ago.
A possible ban - which authorities say would be implemented over the group's use of violence - would be a repeat of the decades-long struggle between the state and the Brotherhood. It also would drain the group's financial resources and allow for mass arrests of its members. That likely would diminish the chances of a negotiated solution to the crisis and push the group again underground.
The Brotherhood has shown no signs of backing down though.
Under the banner of an anti-coup alliance, the group held protests Sunday, though many appeared smaller in scale than others held in recent days. In the coastal city of Alexandria, protesters clashed with residents. In the southern city of Assiut, security forces fired tear gas to disperse hundreds rallying in front of a mosque.
"They think they can end the movement," said Muslim Brotherhood senior member Saad Emara. "The more killings, the more people join us."
However, the government blames Islamists for series of attacks on churches and police stations, increasing public anger against the group.
In his first appearance since the violence began, el-Sissi spoke at length in an hour-long speech about the motives behind ousting Morsi. The general said the Islamist president exploited democracy to monopolize power. He again said the military's action "protected Egyptians from civil war," despite the ongoing violence on the streets.
"We will not stand by silently watching the destruction of the country and the people or the torching the nation and terrorizing the citizens," el-Sissi said in a speech aired on state television. "I am not threatening anyone. ... If the goal is to destroy the country and the people, no!"
The general said that the military didn't seek power but instead "have the honor to protect the people's will - which is much dearer (than) ruling Egypt."
El-Sissi also said Islamists must be included in the country's politics moving forward. A military timetable calls for the nation's constitution to be amended and for presidential and parliamentary elections to be held in 2014.
El-Sissi's speech was an attempt to consolidate internal support in the face of international criticism. In a joint statement Sunday, the presidents of the European Commission and the European Council said it was the responsibility of the army and the interim government to end the violence, warning against the use of force. They said EU will "urgently review in the coming days its relations with Egypt" - meaning much-need financial aid could be on the line.
"We regret deeply that international efforts and proposals for building bridges and establishing an inclusive political process ... were set aside and a course of confrontation was instead pursued," the statement by Jose Manuel Barroso and Herman Van Rompuy read.
They warned: "This path will not succeed."
Nearly two weeks of international diplomacy by the EU, U.S. and Arab nations failed to broker a peaceful end to the standoff. Lawmakers in the U.S. expressed greater discontent Sunday with Egypt - and concern about $1.3 billion in annual military aid it gives the nation.
Egypt also lost one of the few doves in the country's military-backed administration Sunday as Mohamed ElBaradei, who resigned as vice president in protest of the use of force against Morsi's supporters, flew out of Cairo to Vienna. ElBaradei declined to speak to journalists as he left Egypt, where pro-military news outlets have become increasingly hostile toward him.