Thomas Dandois and Valentine Bourrat were detained in early August while making a documentary in the restive eastern region, for Franco-German TV channel Arte.
They are accused of breaking immigration laws, as they did not have journalist but only tourist visas.
Indonesia is deeply sensitive about journalists covering Papua, where a low-level insurgency against the central government has been ongoing for decades. Jakarta rarely grants visas for foreigners to report independently in the region.
Foreign reporters detained for illegal reporting in Papua have in the past been swiftly deported. However Aristo Pangaribuan, the lawyer for the French journalists, said Tuesday that a trial was looking likely.
Dandois was detained at a hotel in the city of Wamena with members of separatist group the Free Papua Movement (OPM), and Bourrat was detained shortly afterwards.
The OPM has been at the forefront of the fight against the central government in the resource-rich but poor, ethnically Melanesian region.