The US-based watchdog cited 13 cases of alleged abuse, including torture, sleep deprivation, severe beatings, sexual abuse and rape threats among people arrested after the July 15 attempted putsch.
"By removing safeguards against torture, the Turkish government effectively wrote a blank cheque to law enforcement agencies to torture and mistreat detainees as they like," Hugh Williamson, HRW's Europe and Central Asia director, said in a statement.
Its report detailed several examples of detainees with bruises and marks on their body and said some lawyers were too scared to record evidence that their clients had been tortured.
In one alleged incident, an Istanbul-based lawyer told the rights group that her client said officers "threatened to rape them and their wives."
The report is based on interviews with 40 people between August and September including lawyers, human rights activists and those who had been detained, HRW said.
The emergency was first imposed a few days after the coup bid then extended for another 12 weeks earlier this month.
It extended detention without judicial review from four to 30 days, and authorised a detainee to be denied access to a lawyer for up to five days, HRW said.
The Turkish government did not immediately respond to requests for comment.
But two days before the report was published, Justice Minister Bekir Bozdag insisted "there is no bad treatment or torture" in Turkish prisons and detention centres.
In a series of Twitter posts on Sunday, Bozdag demanded those making such accusations provided further details on where and when the abuse took place, who the victims were and who the perpetrators were.
He did not name the HRW or any other group as the accuser.
In another, he said Turkish prisons and detention centres were open to international, civil, judicial and administrative checks. "These checks have been made completely," he added.
More than 35,000 people have been placed under arrest since a rogue military faction tried to remove President Recep Tayyip Erdogan from power.
The Turkish government argues it is dealing with an extraordinary threat to the country, but its allies in the West have expressed concern and urged it to act in line with the rule of law.
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