Essam el-Erian, one of the most senior Muslim Brotherhood leaders still at large, was arrested Wednesday in Cairo.
El-Erian is the vice chairman of the Brotherhood's political wing, the Freedom and Justice Party. He had been hiding in a residence in New Cairo, a recently built satellite city of Cairo, according to the Egyptian state news agency MENA.
Egypt's interior ministry commented that a warrant had been issued against el-Erian by the state's general prosecutor, accusing him of "inciting violence" and "aiding criminal acts."
The arrest comes as part of an ongoing move to crack down on the Brotherhood movement by the military-supported government since then-President Mohammed Morsi of the Brotherhood was deposed in July.
Since then, over 2,000 Brotherhood members have been arrested, and at least 1,000 people were killed in clashes in August when government forces cleared two Brotherhood camps in Cairo. Following this, a state of emergency was declared.
In September, an Egyptian court banned the Brotherhood and seized its funds. Morsi and other leaders of the group stand trial for incitement to killing protesters when Morsi was in power.
The US announced earlier this month that it would cut millions of dollars in aid to Egypt to protest the slow pace of democratization by the military government.
Tuesday, a day before the arrest of el-Erian, 27 suspects were arrested on suspicion of planning to assassinate Egypt's interior minister.