Special security laws govern Thailand's Muslim-majority southernmost provinces, where more than 6,500 people, mostly civilians, have been killed in a 12-year insurgency against Thai rule.
Under martial law, which is flanked by an emergency decree, rebel suspects can be detained for six weeks without charge, according to a report by rights groups to be released on Wednesday documenting widespread abuses.
The study, rare research in a dangerous zone cloaked by security forces and insurgents, found 54 cases of physical and mental torture or mistreatment between 2014-15, often at military camps.
"What we have documented is the tip of the iceberg," said Pornpen Khongkachonkiet, of the Cross Cultural Foundation, one of the research groups.
The situation has worsened since Thailand's 2014 coup put the military in power, she added.
"With no accountability or oversight mechanisms since the coup... Interrogation officers have almost a free hand" over detainees, she explained.
The insurgents are seeking greater autonomy from Thailand, which annexed the region more than a century ago, and have employed brutal tactics including indiscriminate shootings, beheadings and bombings.
He was taken Inkayuth military camp, an interrogation centre in Pattani province, where he alleged he was abused over several days.
Army spokesman Pramote Prom-In, dismissed the torture allegations contained in both reports as "imaginary."
"Losing their freedom may be torture for them... But we need to enforce the law," he told AFP.
"Detainees are allowed family visits and arrests are made in front of witnesses," he added.
The military has hailed a record drop in violence in recent months as the result of better intelligence-led operations since it took power and the fruit of tentative peace talks with a number of rebel representatives.
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