The arrest stoked fears of an escalation in the already tense situation in Egypt, where nearly 900 people have died in days of clashes nationwide between security forces and Islamist supporters of Morsi.
In the latest bloodshed, militants killed 25 policemen in the restive Sinai Peninsula, just hours after 37 Muslim Brotherhood prisoners died in police custody.
The interior ministry said police picked up Brotherhood chief Mohamed Badie, 70, near Rabaa al-Adawiya square, where more than 200 Morsi supporters were killed on Wednesday as police cleared their protest camp.
Senior members of the Muslim Brotherhood organization, including Badie, have been accused by Egypt's military-backed authorities of inciting the violence that the deaths of protesters.
And judicial sources said fresh accusations had been leveled against Morsi himself, who has been held in a secret location since the military deposed him on July 3.
Meanwhile, former president Hosni Mubarak won conditional release in the third of four cases against him, but remained in detention on the fourth.
The bloodbath sparked by the crisis showed little sign of abating as militants fired rocket-propelled grenades at two buses carrying police in Sinai on Monday -- the deadliest attack of its kind in decades.
The interior ministry blamed the attack on "armed terrorist groups" and officials later said the border with the Palestinian Gaza strip, near where the attack occurred, would be closed.
Security sources said another policeman was killed in the northern city of El-Arish, bringing to at least 75 the number of security force members killed in Sinai since the army toppled Morsi.
The attack followed the death of 37 Muslim Brotherhood detainees as they were being transferred to a north Cairo jail.
Authorities said they died after police fired tear gas in a bid to free an officer taken hostage by prisoners.
But the Brotherhood, the once-banned movement from which Morsi hailed, held the police accountable, accusing them of "murder".
They said the incident affirmed "the intentional violence aimed at opponents of the coup, and the cold-blooded killing of which they are targets".
BA/BA