Two more prominent Islamist figures have been arrested as a Cairo court met to discuss the release of former president Hosni Mubarak.
Officers held preacher Safwat Hegazy as he reportedly tried to flee to neighbouring Libya disguised as a woman, and Mourad Ali, a spokesman for the Islamist group. Hegazy is believed to be a close ally of the Brotherhood, according to state media.
News of the arrests came as a court convened in Cairo today to consider a petition for the release of Mubarak, who was ousted after a 30-year reign.
Mr Mubarak is appealing against his detention over charges of corruption. He will be re-tried on charges of complicity of the murders of protesters killed in the uprising that deposed him in 2011.
The 85-year-old is currently being held in the Tora Prison in south Cairo.
The arrests form part of a crackdown currently underway, led by Egypt's interim government against the Brotherhood the military ousted former leader President Mohamed Morsi.
A state of emergency is in force across the region after almost 900 people, including more than 100 police and soldiers reportedly killed since Wednesday when the military forcibly cleared by security forces last week, triggering violence that killed hundreds of people.
A bloody attack followed that saw 25 policemen executed during an ambush by suspected militants in the Sinai Peninsula.
Hundreds of Brotherhood members are already detained in custody, including the Brotherhood's former politicians and field operatives, whilst Mr Morsi and his senior aides have been held at an unknown location, incommunicado since the 3 July military coup.
Mr Badie was arrested in an apartment in the Cairo district of Nasr City, close to the site of the pro-Morsi protests.
Badie and his influential deputy Khairat el-Shater, who is also in custody, will go on trial later this month for their alleged role in the killing of eight protesters outside the Brotherhood's Cairo headquarters in June.
The removal of Mr Morsi, Egypt's first democratically elected president, came after four days of mass protests in Cairo and elsewhere demanding he step down for abusing power.
MENA said Mr Hegazy, who joined ranks with the Muslim Brotherhood in campaigning for Mr Morsi's presidential bid, showed no resistance during his arrest and was flown to a detention centre in Cairo.
He was a key speaker at the main pro-Morsi sit-in that was dispersed by security troops last Wednesday in Cairo's Nasr City suburb. He told protesters to hold their ground and promised to deal blows to the military.
He is wanted on charges of instigating deadly clashes last month with security forces outside a Republican Guard building that killed 54 people, most of them Morsi supporters.
The Brotherhood arrests are aimed at crippling the group and weakening its ability to continue street protests.
Over the past three days, the group's near-daily protests since Mr Morsi's removal have diminished, with scattered demonstrations in Cairo and elsewhere attracting only hundreds, or even dozens, of protesters.