Ministry spokesman Khaled el-Khatib said initial reports also indicated at least 322 were wounded, although he gave no details on the circumstances of the killings.
Military spokesmen said gunmen opened fire on troops at the building, killing at least five supporters of Mohammed Morsi and one officer.
A spokesman from Morsi's Muslim Brotherhood, Mourad Ali, and a witness at the scene however said military forces opened fire at dawn on the protesters outside the Republican Guard building. The different accounts could not be reconciled.
Satellite broadcaster Al-Jazeera showed footage from a nearby field hospital of at least six dead bodies laid out on the ground, some with severe wounds. A medic from the area, Hesham Agami, said ambulances were unable to transport more than 200 wounded to hospitals because the military had blocked off the roads.
Al-Shaimaa Younes, who was at the sit-in, said military troops and police forces opened fire on the protesters during early morning prayers. "They opened fire with live ammunition and lobbed tear gas," she said by telephone. "There was panic and people started running. I saw people fall."
Women and children had been among the protesters, she said.
Morsi supporters have been holding rallies and a sit-in outside the Republican Guard building since the military deposed Morsi last week during massive protests against him. The military chief replaced Morsi with an interim president, until presidential elections are held. But Morsi's supporters refuse to recognize the change in leadership and insist Morsi be reinstated. Besides the Republican Guard sit-in, they are also holding thousands-strong daily rallies at a nearby mosque.
Morsi's opponents are also holding rival rallies. They say the former president lost his legitimacy by mismanaging the country and not ruling democratically, leading to a mass revolt that called on the army to push him from office.
Military spokesman Col. Ahmed Mohammed Ali said initial information indicates that gunmen affiliated with the Brotherhood tried to storm the Republican Guard building shortly after dawn, firing live ammunition and throwing firebombs from a nearby mosque and rooftops. One police officer on the scene was killed, he said. Another military spokesman, who declined to be named because he was not authorized to brief reporters, said five from the Brotherhood side were killed.
A statement by the armed forces published on the state news agency said "an armed terrorist group" tried to storm the Republican Guard building, killing one officer and seriously injuring six. The statement said the forces arrested 200 attackers, armed with guns and ammunition.
After declaring the ouster of Morsi last Wednesday, the Defence Minister Abdel-Fattah el-Sissi replaced him with Egypt's chief justice and suspended the constitution until new presidential elections. The transition plan is backed by liberal and secular opponents of Morsi, and had been also supported by the ultraconservative Islamist Al-Nour party and both Muslim and Christian religious leaders.
Soon after the attack report however, Al-Nour party spokesman Nader Bakkar said on his Twitter account his party is withdrawing its support for the transition plan in response to the "massacre."
Associated Press Writer Maggie Michael contributed to this report