Morsi's advisors on foreign and political affairs, Essam Al- Hadad and Ayman Ali, were arrested in their apartment in Heliopolis district, eastern Cairo, the report said.
Egypt's public prosecution issued arrest warrants against the two members of the Muslim Brotherhood in August.
They stopped using their Facebook and twitter accounts, a main platform to incite protests to reinstate what they call " legitimacy," after security forces cracked down in Mid-August on two sit-ins backing the ousted Islamist president. Nearly 1,000 people have been killed and more than 2,000 Islamists have been arrested since then.
As many as 10 armored vehicles have surrounded the building where the two advisors were hiding out, the report added, noting they didn't resist the arrest against them.