A researcher for the EIPR who was detained at the beginning of this year has had his detention renewed for a month and a half.
Zaki, 28, was arrested at Cairo airport on his way into the country in February, blindfolded, taken to an unknown location and beaten and tortured with electric shocks.
Since then he has been in jail pending investigation for allegedly spreading false news and misusing social media.
Zaki was home for a visit from the University of Bologna in northern Italy where he was studying for his postgraduate.
His case raised parallels with that of Giulio Regeni who was tortured to death by members of Egypt's national security agency in 2016.
On Sunday, Zaki appeared in court alongside 700 other people arrested in different cases where his detention was extended.
Human rights advocates have condemned Egypt's use of mass trials to sentence detainees which do not comply with international standards for due process.
The decision came after three senior staff members of the EIPR were released last Thursday following an international outcry over their arrest which included an appeal from Hollywood star Scarlett Johansson for their release.
They were arrested following a meeting with Western diplomats about the human rights situation in Egypt.
Following their release, a terror court froze their assets and a state-run newspaper threatened EIPR founder, Hossam Bahgat.
"It is not unlikely for Hossam to suddenly vanish," wrote former editor Khaled Imam in the publication which has ties to National Security.
"His followers would claim he was forcibly disappeared or detained. But if he does suddenly disappear then most certainly, he will have joined a terror group abroad."