Beltagy, a former member of parliament and head of the Brotherhood's Freedom and Justice Party, was arrested in Giza governorate, just outside of the Egyptian capital, state television reported on Thursday.
Beltagy was wanted on accusations that he incited violence and has been hunted by authorities for nearly three weeks.
He went into hiding earlier this month after authorities violently broke up protest encampments held by supporters of ousted president Mohamed Morsi, who was overthrown by the military on July 3 after days of mass protests against him.
Hundreds died in the crackdown, including Beltagy's daughter, Asmaa.
Most of the Brotherhood's top leadership has been arrested in the nearly two months since Morsi's ouster.
The group's general guide, Mohamed el-Badie, was arrested earlier this month.
He is facing criminal charges for inciting violence, as is his deputy, Rashad al-Bayoumi; the group's top strategist, Khairat al-Shater; and several other senior officials.
Morsi himself has been held nearly incommunicado since he was forced from office.
More than 60 other members of the organization have been detained over the past few days, including relatives of senior leaders.
The son of Khairat el-Shater, the Brotherhood's top strategist, was arrested this week, as was Mohamed Soltan, a US citizen who is the son of outspoken Brotherhood leader Salah Soltan.
SHI/SHI