Banda Aceh – Indonesian police said on Friday they shot and killed a separatist commander in restive Aceh province but denied rebel allegations he'd been tortured to death.

Clashes between security forces and members of the Free Aceh Movement, who have been fighting for independence since 1976, occur almost daily in the resource-rich province on the tip of Sumatra island with both sides trading accusations of brutality.

Police said Abu Arafah, the regional rebel chief for western Aceh, died of wounds after an ambush on Thursday south of provincial capital Banda Aceh, 1,700 km northwest of Jakarta.

"He was shot in a raid on his house. He refused to surrender and tried to run away so our men shot him in the thigh. He died on his way to the hospital," Taufik Sugiyono, an Aceh police spokesman, told Reuters.

"Our troops didn't [mistreat him]. He died because the closest hospital was so far away and the bleeding couldn't be stopped," he added. Another separatist commander confirmed Arafah's death but accused the police of brutality.

"He died of torture not shots. A wounded prisoner should have been taken care of. This is clearly a violation of human rights," said Amri bin Abdul Wahab.

Aceh is one of two separatist hotspots in Indonesia, the other is in the rugged eastern province of Papua where two US teachers and an Indonesian were killed last month.

People living in Aceh blame both sides for human rights abuses but direct most of their complaints at the security forces.

The rebels want independence for the province and say the government has long siphoned off oil and gas reserves but given little in return.

The government has flatly rejected independence but last year granted a special autonomy deal and says it wants to continue with peace talks, although these two-year long efforts have so far failed to halt the killings.

Police have been holding a British and American woman in Aceh since last month accusing them of associating with the rebels and prosecutors are now deciding whether to pursue a case against them.

Briton Lesley McCulloch and American Joy Lee Sadler are suspected of abusing their tourist visas after they were found in possession of rebel material, police have said.