The victims have been subjected to "horrendous abuses," including electric shocks to sensitive areas and rape. The interior ministry has denied any wrongdoing, acknowledging many are in custody after months of detention.
Human rights watchdog Amnesty International on Wednesday published a damning report implicating Egypt's police and judiciary in an "unprecedented spike" in enforced disappearances since early 2015.
The London-based organization said the practice aims to quash dissent. "Enforced disappearance has become a key instrument of state policy in Egypt. Anyone who dares to speak out is at risk," said Philip Luther, the watchdog's Middle East and North Africa director.
The report said "several hundred" Egyptians, many of them supporters of Egypt's first democratically elected president, had been arrested at their homes, then transferred to state security detention centers, where several had been tortured.
"Methods of torture reported by victims and witnesses include electric shocks to the body and sensitive areas, such as the genitals, lips and ears; prolonged suspension by the limbs while handcuffed and naked; and sexual abuse, include rape; beatings and threats," the report said.
Families forced into silence
In one case, the police had said Mohamed Hamdan was "the head of a terrorist cell that targeted policemen" and died in a shootout. But his family told DW that Hamdan was disappeared and killed under torture and that the shootout is a cover-up.
"He had been forcibly disappeared for two weeks when they told us to come identify his body," said Mohamed's younger brother, Hussein. When Hamdan's family saw his body at the morgue, Hussein said they noticed traces of torture and that his feet had been restrained.
Still, family members said they would not call for an investigation. In order to retrieve relatives' bodies, families have to sign papers promising not to talk to the media or request an official investigation.
Hussein said his father was pressured not to press charges against security forces, "They told him, 'You should think of your other sons."
Increase in disappearances
The country's official National Council for Human Rights said it raised 266 cases of enforced disappearances with the Interior Ministry from April 2015 to March of this year.
In January, the Interior Ministry acknowledged that more than 100 people whose relatives complained of an enforced disappearance had been in their custody, adding that they had been lawfully detained. The ministry consistently denies it acts beyond the law.
The majority of those disappeared by state security authorities supported ex-President Mohamed Morsi, who was overthrown by a military coup led by current President Abdel Fattah el-Sissi in July 2013.
El-Sissi's government has designated Morsi's Muslim Brotherhood and its political wing, the Freedom and Justice Party, as terrorist organizations.
In August 2013, the army - led by then-military general el-Sissi - launched a brutal crackdown that left over a 1,000 people dead.
Behaving, while the media watches
"What usually happens is that the policeman gets prosecuted, gets sentenced, to appease popular anger - but only if the media have shed light on the case. Then, when time has passed, the policeman wins his appeal," Mohamed Lotfy, director of the Egyptian Commission for Rights and Freedoms NGO, told DW.
Amnesty's Luther urged the Egyptian presidency to send a clear message to end the practice of enforced disappearances and torture at the hands of law enforcement authorities.
"President Abdel Fattah el-Sissi must order all state security agencies to stop enforced disappearances, torture and other forms of ill-treatment and make clear that anyone who orders, commits or is complicit in such violations will be brought to justice," he said.
ls/kl (AFP, dpa)