The court ordered a freeze on the assets of Nazra for Feminist Studies and its founder Mozn Hassan, and Mohamed Zarea and his Arab Penal Reform Organisation.
The court is investigating civil society groups on suspicion of receiving illegal foreign funding.
Today's decision comes months after an Egyptian court froze the assets of five other human rights defenders and three non-governmental organisations over similar accusations.
The United Nations had said it was "extremely concerned" by the September decision to freeze the assets of the activists and NGOs, which stoked fears of an intensified crackdown on civil society.
The investigation, which began in 2011, caused a diplomatic rift between Washington and Cairo after police closed down several foreign NGOs and sought to arrest their American staff.
In 2014, a court sentenced 43 Egyptians and foreigners in the case to up to five years in prison.