The Malay-Muslim south has been in the grip of a bloody insurgency that has killed nearly 7,000 people over the last 15 years, and allegations of abuse and impunity against the Buddhist-majority Thai state are rife.

The conflict garners little global attention although the majority of the dead are civilians -- both Muslims and Buddhists.

On Saturday afternoon, authorities arrested suspected rebel Abdulah Esormusor, 34, and took him to the infamous Inkayuth detention centre in Pattani province.

He was found unconscious less than 12 hours later after questioning and taken to hospital with severe brain swelling, southern army spokesman Pramote Prom-In said in a statement.

The army is investigating the incident and "if it is found it was a mistake by authorities, those responsible will face severe punishment", he said, before adding there was "no evidence" yet that interrogators caused the injuries.

Inkayuth camp is the Thai army's biggest detention centre in the south, where rebel suspects are taken for questioning and held under the emergency laws governing the conflict-scarred region.

Shadowy insurgents carry out near-daily bomb attacks and shootings in their battle for greater autonomy from Thailand.

But rights groups have also accused security forces of torture and extrajudicial killings, although prosecutions of soldiers fighting in the south are virtually unheard of.

The army vehemently denies allegations of systematic detainee abuse and torture at Inkayuth camp.

Thailand's army can detain suspected rebels for weeks without charge under special powers governing the south.

Critics say the situation worsened under the junta that ruled Thailand from 2014, while peace talks have stalled for years.

A new government with the same junta leader Prayut Chan-O-Cha as prime minister and defence minister was sworn in this month.