CAIRO (Reuters) - Egyptian President Abdel Fattah al-Sisi's government has set up a "parallel system of justice" to crack down on critics and silence dissent through four security and judicial bodies that hold thousands of people for years on vague terrorism charges, Amnesty International warned on Wednesday.

The London-based rights group said the main tools of repression were the Supreme State Security Prosecution, the National Security Agency, special police forces, and counterterrorism courts, noting that these bodies "emerged as a parallel judicial system to arrest, question and prosecute peaceful dissidents."

State Security Prosecution
In a new report, the organization said that Egypt's state security prosecutor routinely abuses the anti-terrorism law to prosecute peaceful government critics and derail fair trial guarantees.

The prosecutor, who is charged with dealing with activities the regime considers a threat to state security, frequently interrogates political and Islamist opponents, including the Muslim Brotherhood.

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The organization's head of research and defense for the Middle East and North Africa, Philip Luther, criticized the Supreme State Security Prosecutor's Office.

Amnesty International's Freedoms Officer Katya Rowe said the organization's report showed the Egyptian prosecutor's office was involved in serious human rights violations, including enforced disappearances and arbitrary detention.

Katia Rowe called on Egypt's international allies not to sacrifice human rights principles for economic, strategic and security interests.

Victims of remand
The report pointed out that many of the detainees are forced to remain in prison for long periods under the name of "pre-trial detention", without any hope of legal delay or open the case before the court.

"Many have been detained for months and years without evidence, based on secret police investigations and without effective treatment."

NGOs say thousands of activists, dissidents, bloggers and journalists are arbitrarily detained in Egypt in inhumane conditions. But Cairo, which has strong international alliances, justifies repression with counterterrorism imperatives, while opponents of Egyptian President Abdel Fattah al-Sisi, who won the presidency in 2014, see him as one of the most authoritarian figures in the Middle East.

More than 1000 days behind bars
Amnesty International's report cited the case of colleague Mahmoud Hussein, a journalist with Al-Jazeera who had been detained for more than three years, despite a court order for his parole.
The Egyptian authorities renewed the imprisonment of colleague Mahmoud Hussein for 45 days, after about 1070 days of detention without trial.

The Egyptian authorities have been detaining Mahmoud since December 2016, charging him with trumped-up charges, including broadcasting false photos and news, and receiving money from outside parties to discredit the country.

Earlier this month, the authorities allowed him to attend the funeral of his father, who died earlier this month, but was sent back to jail without condolences. To release him.

Rami Shaath .. Another detainee
Celine Lubran, the wife of Egyptian human rights activist Rami Shaath, called on France to have its partnership with Egypt conditioned on respect for human rights.

On July 5, Egyptian authorities in Cairo suspended the boycott, divestment and sanctions coordinator for Israel, Rami Shaath, who was an active activist during the 2011 revolution, and his French wife Céline Lubran was deported to her country.

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"They came in the middle of the night. They broke into the building and our apartment, most of them were masked. They had no arrest warrant and they gave us no explanation," Lubran told a news conference in Paris on Tuesday.

"In Egypt, there is an expression used to refer to pre-trial detention," said Lubran. "The detainee is said to be in the refrigerator, and the state can keep detainees there for months or even years."

Lubran confirmed that her husband, accused of "aiding a terrorist group," had been in custody for 150 days, and none of his lawyers had access to his file.

Shaath appeared for the first time on Monday before a judge, during a suddenly scheduled hearing.

"The international observers were unable to attend the session, and Rami was placed in a soundproof glass room.

"We have learned through the press to extend his detention for 45 days," Lubran said, who has been unable to establish any direct contact with her husband since his arrest.

She acknowledged the French authorities' actions to consider the situation of her husband, calling on Paris to "raise the voice" and take a stronger position.

"My husband was arrested in July, and the following month the red carpet of Sisi was brushed at the G7 summit in Biarritz."

Pompeo calls for respect for press freedom
In the same context, US Secretary of State Mike Pompeo on Tuesday called on Egypt to respect freedom of the press, days after Egyptian security forces stormed the headquarters of the independent website "Mada Masr" on the Internet and the detention of three of its staff briefly.

"As part of our long-standing strategic partnership with Egypt, we continue to raise the fundamental importance of respect for human rights and public freedoms and the need for a strong civil society," Pompeo told a news conference.

Mada Misr, which has been raided in recent days, is an Egyptian news site that publishes stories critical of the government after harassment of the media, and publishes materials in both Arabic and English.

"A nine-member force stormed his headquarters at 1:30 pm Sunday, and quickly confiscated the phones and computers of the team members," the website said on Sunday. "The officers refused to reveal their identities."

The website said the three journalists were released from a police station later that day.