Public transport on the main road linking Banda Aceh and the capital of neighbouring North Sumatra province has stopped following attacks on vehicles.
In Jakarta, Foreign Minister Hassan Wirajuda told diplomats that Indonesia's territorial integrity was at stake in Aceh, the country's northernmost province on the tip of Sumatra.
Casualty claims disputed
"GAM forces are moving continuously, and we are tracking them today," senior military spokesman Lieutenant Colonel Achmad Yani Basuki said. "Our attacks are not on specific areas, but wherever we find GAM. In those places, we will carry out attacks," he said.
The military said it had killed four separatists overnight, taking the total since Monday to 12. Six soldiers have been wounded in the fighting.
A spokesman for the Free Aceh Movement (GAM) insisted no separatists had been killed and accused the military of murdering nearly 50 civilians. The military denied killing non-combatants.
|Caught in the crossfire|
Casualty claims have been hotly disputed ever since GAM began fighting for independence in 1976.
But one hospital official in the provincial capital, Banda Aceh, said the military had brought in nine dead bodies riddled with bullets since Monday. They looked like civilians, he said.
"Almost 50 civilians have been killed by the military," said a GAM spokesman, speaking from an undisclosed location. He could offer no eyewitness accounts of troops doing the killing.
The military said a district rebel commander Teuku Ali Said surrendered on Wednesday. Last week another senior rebel commander defected, it said.
Indonesia now has 45,000 troops and police in Aceh. GAM has about 5,000 fighters. Some 10,000 people have died so far in the 27-year-old war.