The New York-based group said in a report that six people arrested in the coastal city of Alexandria in February had reported to relatives that they were tortured with electric shocks and beatings.
They had been accused of protesting without a permit, vandalism and arson, and joining an illegal group.
A police official told AFP that the allegation in the report "was illogical and clearly fabricated."
HRW said that police had initially refused to admit they were holding the detainees for more than a week.
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"Some Egyptian officials have disappeared children and apparently tortured them, then faked arrest records to cover it up," the report quoted HRW's children's rights director Zama Coursen-Neff as saying.
"The authorities have turned a blind eye to the reports of abuse and refused to investigate."
It said six of the detainees told relatives they were suspended by their arms, electrocuted in the genitals and punched.
They had been arrested after an alleged arson attack on a police vehicle and a garage.
"Since 2014, Human Rights Watch has documented National Security officers' frequent use of enforced disappearance and torture, as well as a failure by prosecutors and judges to investigate these violations when defence lawyers raise them.