General Guide Mohammed Badie, the spiritual leader of Egypt’s Muslim Brotherhood, has been arrested in Cairo, officials say.
Reports said Mohammed Badie was detained at a residential flat in Nasr City.
A state of emergency is in force in Egypt amid turmoil following a crackdown on Islamists in which hundreds have died.
Three days of mourning are being held for 25 police killed in Sinai by suspected Islamist militant extremists.
Almost 900 people, including more than 100 police and soldiers, are reported to have been killed in Egypt since Wednesday, when the army cleared protest camps set up by supporters of deposed President Mohamed Morsi, many of them members of the Muslim Brotherhood movement.
On Sunday, 36 Islamist protesters died in a prison van in the capital, Cairo.
Hundreds of members of the Muslim Brotherhood have been detained over recent days.
Mohammed Badie had been on the run as the military-backed interim authorities in Egypt try to suppress protests at the ousting of Mohamed Morsi.
He is facing charges of inciting violence and murder over the killing of eight anti-Brotherhood protesters outside the movement’s headquarters in Cairo last June.
Officials and state media said Mohammed Badie was detained in a flat in Nasr City in north-east Cairo, near the site of one of the protest camps bloodily broken up last week.
Images of Mohammed Badie shortly after his arrest were shown on the private channel ON TV.
The arrest comes days after Mohammed Badie’s 38-year-old son, Ammar, was shot dead during protests in the capital’s Ramses Square.
Mohammed Badie’s deputy, Khairat al-Shatir, was arrested in the days following Mohamed Morsi’s overthrow.
Correspondents say his detention will further ratchet up tensions in the country, where an indefinite dusk till dawn curfew is in place, a leaves a power vacuum at the top of the Brotherhood movement.
The attack on the Sinai police convoy, close to the town of Rafah on the Gaza border, was one of the deadliest on security forces in several years.
It is not clear who carried out the attack. Sinai is home to a range of militant groups, some of which have links to al-Qaeda.
The off-duty police officers were reportedly ordered to leave the buses before being shot in the back of the head.
State television showed their flag-draped coffins arriving by plane in Cairo.
Egypt’s official media has not connected the killings to the Muslim Brotherhood, but the deaths add to the sense of crisis.
In a separate incident, another police officer was killed in the north Sinai town of el-Arish.
Attacks by Islamist militants on the Egyptian security forces have surged in northern Sinai since 2011 – they have been close to daily in recent weeks.
European Union foreign ministers will meet on Wednesday to decide whether to cut some of the billions of euros in aid pledged to Egypt.
Meanwhile, Egyptian prosecutors have added a further 15 days to ousted President Mohamed Morsi’s detention while they investigate fresh allegations against him.
Mohamed Morsi has reportedly been accused of complicity in acts of violence against protesters outside the presidential palace last December. His detention had already been extended by 30 days in a separate case on Thursday.
Meanwhile, a lawyer for another former leader, Hosni Mubarak, has said he hopes his client could be released from prison within the next two days.
Lawyer Fareed al-Dib said Hosni Mubarak had been cleared of one corruption charge and they were waiting for the court to check whether he still had to be held in custody on other counts.
Hosni Mubarak is facing a retrial for corruption and complicity in the deaths of protesters during the 2011 uprising which ended in his removal from power after 30 years.
While it is still no more than a rumor, analysts say his release would be seen by many Egyptians as a signal that the military is rolling back the changes that flowed from the uprising of 2011.