Thomas Dandois was arrested in his hotel in the city of Wamena on Thursday. He was with three members of the Free Papua Movement (OPM), which has fought for decades against the Indonesian government.
It is unclear under which circumstances Valentine Bourrat was arrested.
According to the police, these OPM members come from an area in the centre of Papua where five of them were killed last week during a gun battle with the army. Two policemen were also killed earlier in the week in an ambush.
The OPM rebels accuse the government and the army of exploiting the Papuan, a local ethnic group.
The provincial police spokesperson, Sulityo Pudjo Hartono said the authorities were concerned that the French nationals were part of a plan to create insecurity and instability in Papua.
Foreign journalists who are detained in Papua are usually deported. Hartono said that Dandois and Bourrat were still being held for questioning.
The French Embassy indicated that they were in contact with the journalists, and with the Indonesian Foreign Ministry and the police in Jakarta and in Papua.
Both journalists were working illegally in the country, with tourist visas.
Jakarta’s government rarely issues visas to journalists who want to go to the Papua area.