Egyptian President Abdel-Fattah el-Sissi has given a "green light" to systematic torture inside detention facilities, allowing officers to act with "almost total impunity", an international rights group said.
In a 63-page report, Human Rights Watch said Mr el-Sissi, a US ally who was warmly received at the White House earlier this year, is pursuing stability "at any cost", and has allowed the widespread torture of detainees despite it being outlawed by the Egyptian constitution.
Mr el-Sissi "has effectively given police and national security officers a green light to use torture whenever they please", said Joe Stork, deputy Middle East director at the New York-based group.
"Impunity for the systematic use of torture has left citizens with no hope for justice."
The allegations, the group said, amount to crimes against humanity.
Egypt's Foreign Ministry slammed the report in a statement later on Wednesday, saying it is full of inaccuracies and undermines the sovereignty of the state and the role of its national institutions.
Most of the detainees are alleged supporters of the Muslim Brotherhood group, which rose to power after the 2011 uprising that toppled president Hosni Mubarak but has been the target of a sweeping crackdown since the military overthrew Brotherhood leader Mohammed Morsi in 2013.
Human Rights Watch says Egypt arrested or charged some 60,000 people in the two years after Mr Morsi, who became Egypt's first freely elected president, was overthrown following a divisive year in power.
Hundreds have gone missing in what appear to be forced disappearances, and hundreds of others have received preliminary death sentences.
Widespread torture in a perceived climate of impunity was one of the main grievances behind the uprising that toppled Mr Mubarak.
Mr Stork warned that "allowing the security services to commit this heinous crime across the country invites another cycle of unrest".
Us President Donald Trump has hailed Mr el-Sissi as an ally against terrorism, but last month the United States cut or delayed nearly $300m in military and economic aid, part of an estimated $1.3bn a year the US has given Egypt since it made peace with Israel in 1979.
Based on interviews with 19 Egyptians detained as far back as 2013, the rights group documented abuses ranging from beatings to rape and sodomy.
Human Rights Watch said local rights groups have documented dozens of deaths under torture in police custody.
It said torture sessions are aimed at extracting confessions, collecting information or simply as punishment.
Prosecutors, who are tasked with probing violations, create an "environment of almost total impunity" by either ignoring complaints of torture or threatening abuse themselves.
Human Rights Watch says it found identical methods of torture used in detention facilities across the country, an "assembly line of serious abuse".
After a "welcoming party" of beatings, detainees are stripped naked, blindfolded and subjected to electrical shocks and various stress positions.
In one position, known as the "grill", detainees are hung from a spit-like wooden pole placed atop two chairs.
Officers often move detainees from one room to the other, where different methods of torture are used, such as pulling out nails or electrocuting a detainee while dousing him with water, often until he passes out.
Some detainees said they were placed inside a room dubbed the "fridge" and kept in extremely cold temperatures while wearing nothing but underwear.
"All my nerves were shaking. I wasn't in control of them," Human Rights Watch quoted a detainee as saying, after an intense torture session that included shocking his genitals with electrical wires.
The researchers found five cases in which officers used torture to force detainees to read pre-written confessions, which were filmed and then posted on social media or shown on state TV.
"I gave them the answers they wanted to hear because the electrocution was too much for me to bear," another detainee said.
The Interior Ministry in the past has denied allegations of systemic torture, blaming any abuses on individuals and saying they are held accountable.
Several officers have been tried and convicted of torture, while others have been acquitted.
Egypt has said enhanced security measures are needed to combat Islamic State (IS) and other armed groups that have stepped up attacks since Mr Morsi's ouster.
Mr el-Sissi declared a state of emergency in April after a series of deadly church bombings claimed by IS.
Citing national security, the government has shut down hundreds of websites, including many operated by independent journalists and rights groups.
Judges have been referred to a disciplinary committee for helping prepare an anti-torture bill, and parliament, which is packed with el-Sissi loyalists, passed a law that would cripple the work of independent rights groups.