The suspects were arrested in the town of Timika on Wednesday night, said Papua police spokesman Oni Lebelaw, adding that they were members of the Free Papua Movement (OPM) separatist group.
Among them is Anthonius Wamang, who in 2004 was indicted by then US attorney general John Ashcroft for the August 2002 shooting, in which two American teachers and their Indonesian colleague were killed.
Wamang was allegedly an OPM commander at the time of the attack, which took place on the road leading to a gold and copper mine in Timika operated by US-owned Freeport McMoRan.
"Eight of them, including Wamang, have been flown to the provincial capital of Jayapura for questioning. The other four will also be flown there later today (Thursday)," Lebelaw said.
OPM rebels have been fighting a sporadic and low-level guerrilla war since 1963 when Indonesia took over the huge mountainous and undeveloped territory from Dutch colonisers.