Thomas Dandois, 40, and Valentine Bourrat, 29, were working for Franco-German television channel Arte when they were detained, a spokesman for the French embassy in Jakarta told AFP.
Dandois was arrested yesterday at a hotel in the city of Wamena with three separatists from the Free Papua Movement (OPM), Papua province police spokesman Sulistyo Pudjo Hartono said.
He gave no details on Bourrat's arrest, but said both were reporting illegally on tourist visas.
"We were concerned that (the French nationals') activities were part of a plan to create insecurity and instability in Papua," Hartono said.
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He said the separatists at the hotel were from the highlands of Lanny Jaya district, where five OPM members were killed in a shootout with the military last week.
The shootout came after two policemen were shot dead, killings that were blamed on the separatist movement.
The OPM has for decades waged a low-level insurgency against Indonesian rule over the resource-rich but poor, ethnically Melanesian region.
A French embassy spokesman said: "We are in constant contact with them, we are in touch with the Indonesian ministry of foreign affairs and the police, both in Jakarta and in Papua, to resolve this issue.