The report, submitted to the UN Committee against Torture, tracked the use of methods including "beatings, electrical shocks, sexual violence" and denial of access to medical care by members of the security services.
Egyptian authorities' "use of torture is so widespread and systematic as to amount to a crime against humanity under customary international law," the coalition of six rights groups said.
Torture has been used "as a political tool to curtail dissent" in Egypt's long-running practice of targeting "human rights defenders, minorities, journalists, academics and opposition politicians," according to Mohamed Lotfy, the Egyptian Commission for Rights and Freedoms' executive director.
The coalition submitting the report included the ECRF, the Egyptian Initiative for Personal Rights (EIPR) and London-based human rights organisation REDRESS.
In November the UN committee will review Egypt's record under the UN Convention against Torture.
Cairo has long been criticised for its rights record during the decade-long rule of President Abdel Fattah al-Sisi who oversaw a crackdown on dissent. Rights groups estimate the country has around 60,000 political prisoners.
Many of them, according to rights groups, have been subjected to brutal conditions in overcrowded cells and regularly mistreated by prison authorities.
"Torture is dismissed as merely isolated acts of misconduct instead of being seen for what it really is: a deliberate attack on Egypt's citizens that is a crime against humanity," said Rupert Skilbeck, director of REDRESS.
According to Monday's report, the use of torture is "part of a state policy," enabled by "emergency laws, 'counter-terrorism' laws and policies, and rampant impunity" for violations.
Cairo has regularly denied torturing people in detention.
- US military aid -
The United States has repeatedly criticised Egypt's human rights record, accusing authorities of torture and "life-threatening prison conditions."
Despite such persistent concerns, the administration of President Joe Biden last month approved most military aid to Cairo, in a total package which exceeds $1.2 billion and includes $235 million subject to human rights conditions imposed by Congress.
Secretary of State Antony Blinken, citing national security interests, waved those restrictions but withheld a separate $85 million over rights issues.
However, the new chairman of the Senate Foreign Relations Commitee, Ben Cardin, threatened to block the military funding, in a move rights groups applauded on Sunday.
"This decision is a needed first step... to hold the Egyptian regime accountable for its egregious human rights violations," 14 rights organisations said in a joint statement applauding congressional efforts to pull support from Egypt.
Cardin replaced Senator Bob Menendez, who on Wednesday pleaded not guilty in New York to bribery and extortion allegations involving the Egyptian government.
Since last year, Sisi's administration has made apparent overtures to the decimated opposition, launching a "national dialogue," pardoning political prisoners and releasing detainees.
But ahead of a presidential election in December that Sisi is widely expected to win, experts say the government has done little to actually advance its rights record.
Despite the release of nearly 1,000 political prisoners in the past year, rights groups recorded almost three times as many detained over the same period.
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