"I think the people here have suffered for far too long and it is time we get to grips with the problem.
"I will no longer say that the problems in the south are just for the security forces, this is a matter for the government to solve."
It was Abhisit's first trip to the region since becoming leader last month.
A separatist Muslim insurgency in the Yala, Narathiwat, Pattani and Songkhla provinces and subsequent state crackdown has led to the deaths of more than 3,500 people in that last five years, according to a report published by Amnesty on Tuesday.
It also said that four people had died in the south as a result of being tortured.
Amnesty said the government and army chiefs in Bangkok had issued frequent directives against torture but the abuse was "sufficiently frequent and widespread that it cannot be dismissed as the work of a few errant subordinates in isolated instances".
Amin Kaseng, a local resident, told Al Jazeera that he and his father had been taken from their home by soldiers to a nearby Buddhist temple, where his father was singled out for questioning.
"I heard my father cry out 'I can't take it any longer'. When they threw him back in with us, he had bruises all over his body and his breathing was faint.
"We shouted at the soldiers to take him to a hospital but they ignored us, until my brother shouted; 'He's dead'."
Amnesty also allege that one victim was buried in a pit up to his neck and another had his face submerged in sewage before having a plastic bag forced over his head.
Abhisit has promised to investigate Amnesty's report, but questioned its accuracy.
He said that a 2005 emergency decree in the provinces, giving soldiers and police immunity and allowing detention without trial for up to 30 days, would be reviewed.
Violence ignited in 2004 with a raid on a military base, bombings, arson attacks and shootings.
No group has claimed responsibility for the attacks and no political demands have been made.
But the targeting of Thai state symbols - including teachers, security forces and government buildings - has led to the violence being described as having a separatist objective.
The provinces have more in common with neighbouring Malaysia than Thailand, having an 80 per cent Muslim population and speaking Malay, rather that Thai.
They were an independent sultanate until being annexed by Thailand about a century ago.