The Brotherhood members were reportedly meeting to discuss sponsoring the families of detainees when the police stormed the building. The victims` families said the men were unarmed and had been taken into custody earlier in the day but were released after gaving fingerprints.
Egypt`s interior ministry, however, said the men were fugitive leaders who were plotting attacks - something the group denies - and said the group included two men who had previously been sentenced to death.
In a statement, the interior ministry said that investigators found weapons, 43,000 Egyptian pounds ($5,300), documents and memory cards and that the group was plotting attacks on the army, police, judiciary, and media.
Pro-Muslim Brotherhood Mekameleen TV said the leaders were detained inside a home and "killed in cold blood without any investigation or charges".
`Dangerous curve`
In a statement following the deaths, the group described the killings as "a significant development with serious repercussions" and said it held "the criminal [Egyptian President] Abdel Fattah el-Sisi and his gang fully responsible for these crimes and their consequences".
"Rise in revolt to defend your homeland, your lives and your children," the statement said, adding: "This murderer is now executing the largest and most horrid massacre against this homeland. Oust the heinous murderer. Destroy the castles of injustice and tyranny. Reclaim Egypt once again."
The group said the incident "pushes the situation onto a very dangerous curve and makes the entire scene highly volatile".
The deaths came as Egypt experienced its deadliest fighting in years.
More than 100 fighters from an armed group, the Province of Sinai, and 17 soldiers were killed after simultaneous assaults on military checkpoints in North Sinai on Wednesday.
The Province of Sinai, formerly known as Ansar Beit al-Maqdis, pledged allegiance to the Islamic State of Iraq and the Levant (ISIL) group in November last year.
Some security sources put the death toll for army and police much higher than the official figure.
On Monday, Egypt`s prosecutor-general was assassinated in a car bomb bearing the hallmarks of the Province of Sinai.
In response, Sisi ordered his cabinet to introduce tougher laws to tackle what he called terrorism.
Crackdown continues
Meanwhile, at least 75 female students were suspended from Egypt`s al-Azhar University over what an official at the institution said was their "involvement in acts of violence and in conspiring against the university".
Ahmed Hosni, the deputy head of al-Azhar, a prestigious religious institution, told local media on Wednesday that a total of 200 female students had been suspended from the university branches in Cairo and other provinces.
Hundreds of Egyptian students with perceived links to the Muslim Brotherhood have been dismissed from universities since Sisi led a military coup that overthrew Mohamed Morsi, Egypt`s first democratically elected president and former leading member of the Muslim Brotherhood, in 2013.
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