Military spokesman Ahmed Aly said in a press conference on Monday afternoon that army and police forces protecting the Republican Guard headquarters were attacked on Monday by armed groups.
According to Aly, pro-Morsi protesters, who have been gathering outside the Republican Guard headquarters for days, used live ammunition and birdshot against security personnel.
He added that at the time of the attack, another group was shooting from atop a building on Al-Tayaran street, where the military facility is located.
"A colleague is in Maadi hospital undergoing a four-hour surgery; he was shot with live ammunition to the head, which caused his skull to fracture," said Aly.
Aly said that the officer's injury proves that there was firing from building rooftops.
The spokesman also criticised footage circulating on satellite channels of Islamist protesters holding bullet casings and claiming they were fired by the army.
Aly stated that the ammunitions were fake, adding that it isn't possible that the bullets were fired by security forces given that once a bullet is shot, the casing falls next to the shooter.
He also denied pro-Morsi protester's claims that the military killed any children.
"Religious groups spread pictures showing children [killed]...how could children have been involved in that hour of the night," said Aly, who added that the pictures used were of Syrian children taken in March 2011.
The military spokesman went on to accuse "certain factions" of inciting violence, as a video of Brotherhood-affiliated preacher Safwat Hegazy was screened in the background.
The video, which has gone viral on social networks, contains a threat of "escalation" from Morsi supporters if the former president is not reinstated.
"Threatening Egypt's national security will not be allowed," Aly said, referring to escalating violence in Sinai, and he added that the army has been deployed in a number of areas Monday with the intention to protect Egyptian lives and vital institutions.
However, Aly also stressed that protesters at Rabaa Al-Adawiya and in other squares are Egyptian citizens and "brothers."
"We call on them to remain peaceful because it is not in anyone's benefit to harm army headquarters; the armed forces and the state promise that no one will be hunted down and that there will be no extraordinary measures taken," he added.
In response to a question about possible splits within the army, Aly vehemently denied the claim, saying it has been used to enact a "psychological war."
"Claims were made that there are huge splits within army, these are all lies attempting to weaken the armed forces or make people lose faith in the army; since its establishment, the Egyptian army has never suffered divisions," said Aly.
He added that the army has arrested a man who was videotaped wearing a military uniform and claiming to be a member of the "free Egyptian army" while threatening people.
At least 51 people were killed and 435 injured in clashes on Monday morning between Morsi supporters and the army. The Muslim Brotherhood said a peaceful pro-Morsi sit-in was attacked by the military during dawn prayers, while the military stated that an "armed terrorist group" attacked the Republican Guard headquarters, leading to the deaths.
The Muslim Brotherhood has been leading a sit-in for several days in front of the Republican Guard headquarters to demand the return of deposed president Mohamed Morsi.
Initial investigations by the prosecution found remains of Molotov cocktails and bullet and birdshot casings at the site of the clashes.
Interior ministry spokesman General Hani Abdel-Latif also spoke at the press conference, echoing Aly's statements regarding the "attack" on the Republican Guard headquarters.
Abdel-Latif stated that one army lieutenant and one conscript was killed in clashes.
"I assure Egyptians that there is full coordination between the police and the army in order to protect the people," said Abdel-Latif, adding that so long as Egypt is free and democratic, the police will strictly confront any law-breaking.
"The people now understand that the police is innocent of all these accusations" he said, referring to prison breaks and sniping down of protesters during the January 25 revolution.
Al-Jazeera correspondents could not attend the press conference after being expelled by fellow reporters accusing the Qatari-owned channel of bias.