Egypt's largest opposition coalition, the National Salvation Front (NSF), has expressed its "deep sorrow" over the death of dozens of people early on Monday outside the Republican Guard barracks.
In a statement it issued on Monday afternoon, the NSF condemned "all acts of violence," including assaults on military barracks and army officers.
At least 42 were killed and 322 injured in bloody clashes between army forces and pro-Morsi protestors outside the Republican Guard compound, the health ministry reported Monday morning.
The Egyptian army said one officer died and 40 soldiers were injured, including eight in critical condition.
According to the military, "a terrorist group" tried to storm the military building.
Soldiers returned fire when they were attacked by armed assailants, a military source said.
However, the Muslim Brotherhood's FJP, which had been holding a sit-in at the army facility at the time of the clashes, issued an official statement saying "peaceful protesters were performing the Fajjr (dawn) prayers" when the army "fired tear gas and gunshots at them without any consideration for the sanctity of prayers or life."
The National Salvation Front has urged prompt investigation into the incident.
Meanwhile, Al-Azhar, Egypt's 1000-year-old seat of Islamic learning, has condemned the "painful incident," which it says will portend a dark time of strife.
Egypt's Rebel campaign, the main force behind calls for the 30 June protests culminating in Morsi's ouster last Wednesday, condemned what it perceived as vengeful attempts by political Islamists against the army.
Mohab Doss, a group's spokesman, claimed the incident was a "reaction" by the army to "intimidation" by Islamist groups.
However, Doss added "the whole truth of what really happened should be uncovered through an independent investigation."