The New York-based rights group said in a report that security services in the North African country used torture as a “systematic practice” against suspected opponents of the government.
Egypt’s foreign ministry said the HRW report was based on undocumented testimonies.
Ministry spokesman Ahmed Abu Zaid said it ignored steps the government had taken on human rights and accountability for individuals involved in torture cases.
Rights groups have regularly accused Egyptian security services of practising torture, something the interior ministry has denied.
“Human Rights Watch believes the torture epidemic in Egypt likely constitutes a crime against humanity, due to its widespread and systematic practice,” the group said in the report.
It said it had interviewed 19 former detainees who detailed the methods of torture, which include electrocution.
Police also handcuffed suspects and suspended them by their arms.
In another position called the ‘chicken’ or ‘grill’, “officers placed a stick or bar behind the suspects’ knees, wrapped their arms around the bar from the other side so that the bar laid between the crook of their elbows and the back of their knees, and tied their hands together above their shins to secure them in the position,” HRW said.
The bar was then lifted, placing the suspects in a position “resembling a chicken on a rotisserie spit”.
The report quoted a former detainee alleging police “repeatedly raped” him with a stick.
Egypt’s government has acknowledged “individual” cases of torture in recent years, and several policemen have been tried and sentenced for violent deaths in detention.
Police abuses fuelled a 2011 uprising that unseated veteran autocrat Hosni Mubarak and ushered in years of political instability.
In 2013, then army chief Abdel Fattah al-Sisi overthrew Mubarak’s unpopular Islamist successor Mohamed Morsi, unleashing a bloody crackdown on his Muslim Brotherhood movement.
Jihadists have since launched a deadly insurgency that has killed hundreds of policemen and soldiers.
Sisi, elected president in 2014, asked the police to crack down on abuses after a spate of violent deaths in prison and police shootings that sparked protests.
In February last year, a court sentenced a policeman to eight years in prison for beating to death a veterinary surgeon in custody in the Suez Canal city of Ismailiya.
In December 2015, a court in the Nile delta city of Tanta sentenced two policemen in absentia to life in jail for killing a man in custody.
The same month, a court sentenced two secret policemen to five years in prison for beating to death an imprisoned lawyer in a Cairo police station.
In its report, HRW recommended Sisi tackle what it called a “torture epidemic” and task the justice ministry with appointing a special prosecutor to investigate complaints of abuse and prosecute them.
Failing that, it urged “UN member states to investigate and, if appropriate, prosecute in their own courts Egyptian security officers and other officials accused of committing torture or allowing it”.
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