Egyptian forces secured and cleared a Cairo mosque that had become the epicenter of Saturday's confrontations between protesters and the military, interior ministry spokesman Hani Abdel-Latif said.
Hundreds of supporters of deposed President Mohamed Morsy had been holed up in the Al-Fateh mosque in central Cairo since overnight.
Without food or medical supplies, but fearful of reprisals if they walked out, the protesters earlier rebuffed the military's request for them to clear the building. The situation escalated as security forces fired at the mosque's minaret, claiming there were snipers firing at them.
In the end, the security forces were successful in securing the place.
The clashes at the mosque had threatened to pull Egypt into another day of widespread violence on Saturday.
Political unrest preceded the military coup that ousted Morsy, and his supporters have held massive rallies against the interim government and its supporters.
Both sides blame each other for instigating violence.
"We are not facing a political struggle," interim presidential adviser Mustapha Higazi said. "We are facing war waged by extreme forces."
The spokesman referred to the protesters as terrorists and warned that "what we see in the streets will not be accepted."
The government urged pro-Morsy protesters to "come to their senses" and unite Egyptians.
"We express our deepest sorrow and offer our condolences to those who have their blood spilled," Higazi said.
At least 173 people have been killed across the country since Friday's mass protests began, the government said.
It was an especially bloody week in Egypt, as the interim government put in place by a military coup seeks to restore stability to the country while Morsy supporters fight to restore the democratically elected former president to power.
With no end to the clashes in sight, the pressure on the international community to act increases, raising questions about aid and diplomacy in North Africa and the Middle East.
The government stepped up its rhetoric Saturday, blaming the protestors -- particularly those affiliated with the Muslim Brotherhood -- of attacking police stations, churches and civilians.
The future of the Muslim Brotherhood and others will be subject to evaluations regarding their legal status, Higazi said.
Members of the Muslim Brotherhood who have not been involved in violence and who would like to "join the peaceful Egyptian march toward the future" would be welcomed, but others will face the law, he said.
"We are not in the effort of dissolving anyone, or preventing anyone from being active in the public domain, but are trying to make sure everyone is legalized according to Egyptian law," he added.
The interim government spokesman also accused the international media of bias and telling an incomplete story.
Inside the Al-Fateh mosque
Hundreds of protesters defied a government-imposed curfew Friday night and stood fast at Ramses Square. The government had warned that those breaking curfew would be dealt with "firmly."
But security forces appear to have acted with restraint overnight, when 1,000 people reportedly took refuge inside the mosque located on the square.
During clashes on Friday -- which protesters had dubbed "a day of anger" -- the building had served as a makeshift morgue and field hospital for the pro-Morsy protesters.
The military offered to provide safe passage out for those inside the mosque, but the protesters said they feared that they would be attacked by pro-government supporters aligned with the military who were also outside the mosque.
The military told the protesters inside the mosque that they would be taken to an unspecified location, said Hanan Amin, a doctor who spoke with CNN from inside the mosque.