El-Beltagy had been in hiding since a police crackdown on supporters of ousted president Mohamed Morsi conducting a sit-in at the Rabaa al-Adawiya mosque in Cairo, Ahram Online reproted.
His 17-year-old daughter, Asmaa, died in the crackdown.
He was arrested in a rural area of Giza.
On Wednesday, el-Beltagy appeared on the al-Jazeera broadcasting network. Speaking on a pre-recorded video, he condemned what he called a military coup that led to the ouster of Morsi, a member of the Muslim Brotherhood.