In a joint report, Amnesty and Human Rights Watch (HRW) accused Turkish police and the armed forces of using the state of emergency declared by President Recep Tayyip Erdogan after the earthquake as a "licence to torture".
In a response before the report was published, the Turkish justice ministry said Ankara had "zero tolerance" for torture but dismissed the findings without responding specifically to them, Amnesty and HRW said.
The report said one person died in custody after being tortured.
It said all the incidents occurred in the 10 provinces covered by the state of emergency but mostly concentrated in Antakya city, Hatay province, one of the areas worst hit by the February 6 quake.
Hugh Williamson, Europe and Central Asia Director at HRW said they were a "shocking indictment of law enforcement practices".
"Law enforcement officials are treating the state of emergency for the natural disaster as a licence to torture, otherwise ill-treat and even kill with impunity," he added in a statement.
Esther Major, senior research adviser for Amnesty International's Europe office, told AFP: "We recognise the size of the catastrophe that has happened, but within that context, a state of emergency must not lead to lawlessness and impunity, to torture and other ill-treatment."
- 'Resort to prohibited means' -
The groups said they had interviewed 12 victims of alleged torture and other ill treatment and reviewed video footage of 13 such cases involving 34 male victims.
They said in four cases, the victims were Syrian refugees and the attacks bore signs of additional xenophobic motivation.
The report found in the majority of cases, victims were not taken into official custody, but immediately beaten or made to lie or kneel down while being kicked, slapped and sworn at for prolonged periods. In only two cases has there been any subsequent investigation.
One Turkish man, Ahmet Guresci, 27, died after being arrested along with his brother Sabri and then being subjected to torture including attempted anal rape with police batons.
Sabri Guresci was later released pending the investigation but three gendarmes have since been suspended over his brother's death, the rights groups said.
While emphasising Turkey's zero tolerance policy on torture, the justice ministry told the rights groups their findings were "vague claims devoid of a factual basis" and did not directly address them.
Emma Sinclair-Webb, HRW associate director and Turkey director, said said the 13 cases documented by the groups represented just the "tip of the iceberg".
"We have to admit there was security challenges, with theft and looting," she told AFP.
"However, the way of dealing with that is not to resort to completely prohibited means, with one case resulting in a death in custody."
The 7.8-magnitude quake and aftershocks killed more than 55,000 people across southeastern Turkey and parts of war-torn Syria.
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