(Beirut) – At least five people pardoned in late September 2015 by President Abdelfattah al-Sisi of Egypt are still being held three weeks later. Many more not covered by the pardons remain unlawfully detained with little chance of release.

On September 23, al-Sisi pardoned 100 prisoners, including journalists, those in ill-health, and dozens who had been arrested for protesting. At least four of them are apparently still being unlawfully held, while a fifth awaits release for procedural reasons, said the Front for the Defense of Egyptian Protesters, a legal group that defends detainees. Thousands of other people charged with crimes related to political opposition are facing unfair legal proceedings, including many who are unlawfully detained or sentenced merely for exercising basic rights such as freedom of assembly and association.

Al Jazeera television journalist Mohamed Fahmy (R) celebrates with his wife Marwa Omara (2nd R) with colleague Baher Mohamed and his wife Jihan after being released after being released from Tora prison, in Cairo, Egypt, September 23, 2015. © 2015 Reuters

“Some Egyptian authorities are so intent on stifling opposition that even those lucky enough to be singled out for clemency by al-Sisi remain in prison,” said Nadim Houry, deputy Middle East and North Africa director. “Even if these pardons had gone off smoothly, freeing 100 people is a drop in the bucket when Egypt is jailing thousands.”

Among those who remain detained despite pardons are two female Mansoura University students whom security forces arrested in November 2013 as they broke up clashes on their campus between opponents and supporters of the Muslim Brotherhood. A judge sentenced each of them to two years in prison for belonging to the Brotherhood, which government prosecutors routinely label a terrorist group, though no competent court has designated it as such. Although al-Sisi pardoned them, Mansoura Prison officials have refused to release them because their appeal of the sentence is pending before Egypt’s highest appeals court.

Al-Sisi issued the pardons five days before addressing the United Nations General Assembly, and his decision appeared to be aimed at resolving high-profile cases that have received the most international attention.

Among those pardoned were Mohamed Fahmy and Baher Mohamed, two Al Jazeera journalists sentenced to three years in prison in August for aiding the Muslim Brotherhood, and Shadi Ibrahim, a student convicted alongside them for allegedly being part of their plot.

At least 42 of those who received pardons were serving sentences for protesting – most of them had been arrested specifically for challenging a ban on protests issued by a military-backed interim government in November 2013. They included Yara Sallam, a researcher for the Egyptian Initiative for Personal Rights, a leading local rights group, and Sanaa Seif, a human rights activist. 

Despite the pardons, thousands of people remain convicted or detained on charges that are based on flawed investigations or false evidence, or for reasons solely related to exercising basic rights.

Though al-Sisi pardoned 18 people who were arrested together in November 2013 for protesting in front of the Shura Council, Egypt’s upper house of parliament, he did not pardon Alaa Abd al-Fattah, a prominent activist sentenced to five years for participating in the same protest. Al-Sisi also did not pardon Ahmed Abd al-Rahman, who witnesses said tried to protect women at the same protest from being attacked by men who later turned out to be police wearing civilian clothes. He was sentenced to five years for breaking elements of the anti-protest law that prohibit assault, “thuggery,” blocking roads, and destroying public property. Local human rights groups have said that prosecutors presented no evidence that Abd al-Rahman committed any act besides being present at a protest, which should not be a crime.

Two other young men who, like those who were pardoned, were serving three-year sentences for participating in the Shura Council protest, did not receive pardons. These two men were retried separately from the main group of defendants and were being held in a different prison, said Mona Seif, an activist whose brother and sister were both sentenced in the same case. Seif said she believed that the president’s office did not “properly” check the case file and was simply unaware that the two men were part of the same case.

Despite issuing pardons for Fahmy, Mohamed, and Ibrahim – after deporting their co-defendant, the Australian journalist Peter Greste, in February 2015 – al-Sisi did not pardon two of Ibrahim’s student colleagues sentenced alongside him: Khaled Abd al-Raouf and Souhaib Sa’ad, who had filmed protests on their smartphones and sold the footage to media outlets through an agency. Throughout their initial trial and a subsequent retrial, prosecutors presented no evidence that any of the defendants in the Al Jazeera case committed criminal wrongdoing.

In June, officers from the Interior Ministry’s National Security Agency forcibly disappeared and allegedly tortured Sa’ad, who is currently standing trial in a military court for allegedly belonging to a terrorist cell.

At least 18 Egyptian journalists remain detained for carrying out their work, most alleged to have ties to the Muslim Brotherhood, according to the Committee to Protect Journalists. Some of them were included in a mass trial before a special national security court in April that sentenced more than a dozen journalists and spokesmen to life in prison, and one journalist to death, for their alleged role in spreading Muslim Brotherhood propaganda after the bloody dispersal of the pro-Brotherhood Rab`a al-Adawiya sit-in in August 2013, following the ouster of Mohamed Morsy as president.

A photojournalist, Mahmoud Abou Zeid, also known as Shawkan, has been held since he was arrested while covering the Rab`a al-Adawiya dispersal. After he spent more than two years in pretrial detention – more than the time allowed under Egyptian law – a judge referred Abou Zeid’s case to criminal court in September 2015, and his trial is set to begin in December. The authorities should immediately release Abou Zeid, Human Rights Watch said.

Al-Sisi pardoned three men – Omar Hazeq, Islam Hassanein, and Naser Abu al-Hamed – who received two-year sentences for allegedly assaulting police during a December 2013 protest against impunity for the officers who killed Khaled Said, an Alexandria man whose death helped spark the 2011 uprising. But he did not pardon the human rights lawyer Loay al-Kahwagy, who also had been sentenced to two years for participating in that protest. Police used a firehose and teargas against the protesters, media reports said. Video shows riot police assaulting the group with batons.

“The release of prominent activists and journalists should not whitewash Egypt’s recent record of detaining peaceful activists, from secular protesters to Muslim Brotherhood members,” Houry said. “At the current rate of detention, it will take many more pardons to empty Egypt’s jails of people unfairly detained.”

More details about the four prisoners who have received pardons but not been released:

Menat Allah Mostafa and Abrar `Ala’ al-Anani, two 18-year old female students at Mansoura University, were arrested in November 2013 after clashes erupted on their campus between opponents and supporters of the Muslim Brotherhood. They sought safety in an office of the university’s pharmacy department, but security forces called in to halt the clashes arrested them. In May 2014, a special national security court sentenced both to two years in prison for belonging to the Brotherhood, which prosecutors routinely label a banned terrorist group. Because Egypt’s highest appeals court accepted their case, Mansoura Prison officials have refused to release them even though they have been pardoned. Since they face no other charges, the prison authorities appear to have no legal basis to detain them and should release them.

Asmaa Abd al-Aziz Shehata – A mother arrested at her home alongside her two sons in November 2014 and accused of assaulting the police and of membership in a group that aims to disrupt public peace and safety. Shehata suffers from schizophrenia, but prosecutors have refused to acknowledge medical and insurance papers detailing her illness, and lawyers have received little information about her health condition since her arrest. The presiding judge has repeatedly renewed her pretrial detention order. On October 13, prison authorities did not bring Shehata to her regular detention hearing for unknown reasons, and the judge postponed the hearing to October 26. Since she is still being held on the charges for which she has been pardoned, she should be released.

Mohamed Talaat – A 66-year-old man who was pardoned because of ill-health. Mansoura Prison authorities have yet to release him for unknown reasons, lawyers said.

In addition, Mo’min Mohamed Abd al-Tawwab was arrested in the vicinity of a June 2014 march in front of Cairo’s Ettihadeya Palace that was expressing opposition to a government ban on protests issued the year before. According to Freedom for the Brave, an independent group that tracks political detentions, Abd al-Tawwab was passing through the area on his way to undergo an operation on his eye and was “randomly” arrested. Abd al-Tawwab was pardoned along with 22 co-defendants, but the authorities have not released Abd al-Tawwab because of a three-month sentence handed down to him in absentia in a separate case. His lawyers have applied for an automatic retrial permitted under Egyptian law in such cases, and prison authorities have transferred him to Heliopolis Police Station in Cairo pending his release.