The 60-page report by the London-based rights group details how Egypt's Supreme State Security Prosecution, or SSSP, has become increasingly central to President Abdel-Fattah el-Sissi's sweeping crackdown on dissent.
"In Egypt today, the Supreme State Security Prosecution has stretched the definition of 'terrorism' to encompass peaceful protests, social media posts and legitimate political activities," said Philip Luther, the group's Middle East and North Africa director.
Concertgoers were accused of terrorism for waving rainbow-colored flags. A journalist charged with "broadcasting false news" was detained repeatedly for three years. A human rights lawyer was arrested for joining a protest he says he didn't attend. Several Christians were imprisoned for "aiding a terrorist group," a reference to the outlawed Muslim Brotherhood organization.
"Ridiculous" prosecutions have proliferated, said report author Hussein Baoumi.
Citing these cases and over a hundred others, Amnesty International said the SSSP, a secretive agency comprised of just a few hand-picked judges, is abusing its legal powers as a counterterrorism branch to stifle political dissent.
"There's no judicial oversight. We're talking about a completely closed circuit," Baoumi said. "If these cases were referred to trial, people would be acquitted at once," as the state's accusations are based on confidential police reports, he added.
Egyptian security forces carried out a harsh crackdown in September to stamp out small but rare anti-government protests. The SSSP played a critical role in sweeping up thousands of people on charges of terrorism, the report said.
The prosecution agency renews people's detentions for months and years without evidence, denying them access to lawyers and a fair chance to appeal, it added.
Amnesty said SSSP investigations into allegations of torture and enforced disappearance by the police intelligence division amount to a whitewash. The SSSP routinely buries evidence of police abuse and gives credence to confessions extracted with torture, it said, drawing on court documents and interviews with dozens of witnesses.
Under el-Sissi, Egypt has seen a "meteoric rise" in cases prosecuted by SSSP, according to Amnesty. The report drew attention to the expansion of the branch's covert role since a court declared indefinite administrative detention unconstitutional in 2013.
There was no immediate comment from the government on Amnesty's report, but authorities have repeatedly denied charges of violations or police brutality. Authorities say they are fighting terrorism and have accused rights groups of working with foreign entities to undermine the state.
El-Sissi led the military's removal of the country's first democratically elected president in 2013 after his one-year rule proved divisive, sparking nationwide protests.
The general-turned-president has overseen an unprecedented political crackdown, silencing critics and jailing thousands.
"Our goal with this report is to make it very clear that when someone is accused of terrorism in Egypt, the international community cannot take it at face value," Baoumi told The Associated Press. "More likely, that person was arrested for peacefully expressing an opinion."
Late Tuesday, police made six new arrests — including three journalists — in central Cairo. Mohamed Saad Abdel Hafiz, a board member of Egypt's journalists' association, wrote a post on social media about the arrests, listing the journalists as Solafa Magdy, Hossam el-Sayyad and Mohamed Salah.
In Washington, a senior State Department official called on Egypt "to ensure journalists can work without threats of imprisonment and intimidation." Assistant Secretary for Near Eastern Affairs David Schenker told reporters Tuesday that "as part of our long-standing strategic partnership, we continue to raise the fundamental importance of respect for human rights."
For decades, the U.S. has been Egypt's largest weapons supplier, with over a billion dollars in military aid each year.