Five Islamist figures have been arrested while attempting to flee Egypt via the southern border, a military spokesman announced via Facebook.
Former Shura Council member and head of Gamaa Islamiya's Building and Development, Safwat Abdel-Ghani, was among those arrested late on Sunday.
Meanwhile, the pro-Brotherhood National Alliance to Support Legitimacy (NASL) said security forces have arrested Nasr Abdel-Salam, acting head of the Building and Development Party.
Last year, prosecutors ordered the arrest of Muslim Brotherhood Supreme Guide Mohamed Badei and nine Islamist figures, including Abdel-Ghani, for allegedly inciting violence at the Republican Guard headquarters.
Gamaa Islamiya was responsible for the assassination of president Anwar Sadat in 1981. It also allegedly murdered 58 tourists and four Egyptians in an attack in Luxor in 1997.
The group formed a political party after the 2011 revolution and won 13 seats in the Shura Council election of 2011-12.
It has played a key role in the National Alliance to Support Legitimacy, which calls for the reinstatement of deposed president Mohamed Morsi and the 2012 constitution.
Some critics say the group, along with the Brotherhood, has been involved in recent terrorist attacks across the country.
There has been a crackdown on prominent leaders and supporters of the Islamist President Mohamed Morsi since his ouster in July 2013.
Morsi faces a number of charges, including espionage and breaking out of prison in the January 2011 uprising.