Egypt is enduring bloody internal strife, with about 900 people killed, including 100 police and soldiers, after the authorities broke up Brotherhood protest camps in Cairo last week.
Mohamed Badie, 70, the Brotherhood's general guide, was taken from an apartment in Nasr City in north-east Cairo yesterday, the area where protesters demanding ousted Islamist president Mohamed Mursi's reinstatement had staged a vigil for six weeks before they were violently dispersed.
He was charged in July with incitement to murder during protests before Mr Mursi's overthrow and is due to stand trial together with his two deputies.
Footage circulating on local media showed the bearded Brotherhood leader sitting grim-faced on a sofa in a grey robe, hands folded in his lap,
The release of the images seemed to be designed to humiliate the Brotherhood's most senior chief, whose arrest means the top echelon of the Islamist movement is now behind bars.
After decades as an outlawed movement, the Brotherhood emerged as the best-drilled political force after Hosni Mubarak's fall in pro-democracy protests in 2011.
Now the state accuses it of al Qaeda-style militancy and subversion, charges it vehemently denies.
The whereabouts of many other senior Brotherhood politicians are unknown. Those who had been posting frequently on social media have stopped in the last two days. Arrests have extended beyond Cairo, capturing provincial leaders of the movement.
The Brotherhood condemned the detention of Mr Badie, whose 38-year-old son was killed on Friday in Cairo clashes.
It said "When the hand of oppression extends to arrest this important symbol, that means the military coup has used up everything in its pocket and is readying to depart."
Tamarod, the youth organisation that orchestrated the street campaign against Mr Mursi, hailed Mr Badie's detention.
A spokesman said: "Arresting Badie is an important step on the path of the revolution, fighting terrorism and dismantling the terrorist group by arresting its leaders."
The state news agency said Mr Badie was taken to Tora prison on the southern outskirts of Cairo, where other Brotherhood leaders are held, as well as former president Mr Mubarak.
On Monday, a court ruled Mr Mubarak, who was arrested after his overthrow in 2011, could no longer be held on a corruption charge and a petition for his release on bail will be examined by a court today, judicial sources said.
Mr Mursi has been held in an undisclosed location since the army toppled him on July 3 following mass protests against him.
The Brotherhood, which renounced violence decades ago, has promised peaceful resistance to the army takeover.
Mr Mursi was already facing accusations stemming from his prison escape during the anti-Mubarak revolt. These include murder and conspiring with the Palestinian Islamist group Hamas.
United Nations Secretary-General Ban Ki-moon called on the authorities to release Mr Mursi.
The turmoil in Egypt has alarmed the US and the European Union, but Israel and some Gulf Arab states led by Saudi Arabia have urged the West not to punish Cairo's new rulers.
The US urged Egypt not to ban the Brotherhood, an option floated in the past week by the interim prime minister.