The police chief of the Lanny Jaya area, senior commissioner Adolf Beay, confirmed that his officers had detained one journalist working in the Papuan highlands.
''He was using a tourist visa but in fact he was doing journalistic work,'' Mr Beay said.
The French embassy in Jakarta later confirmed there were two journalists, Thomas Dandois and Valentine Bourrat, in custody in Jayapura.
''They were journalists doing a documentary for the TV channel Arte,'' press attache Dominique Roubert said.
It is understood the documentary was about the Papuan independence movement, and the pair were caught with three activists from what Indonesian media has identified as the Free Papua Movement (OPM).
Mr Roubert said the embassy had been in contact with the journalists, who were being interrogated by police but otherwise had been ''well treated''.
The embassy was also in contact with Indonesian police.
''We are trying to resolve the problem as quickly as possible,'' Mr Roubert said.
The Papuan police spokesman, senior commissioner Sulistyo Pudjo, said Dandois, 40, was arrested on Wednesday in the company of three members of the OPM.
''We were worried that his activities here were part of an effort to destabilise Papua,'' Mr Pudjo said. He was concerned, he said, that ''foreign journalists deliberately manipulate the security situation'' in the province.
''We’ll work out which laws should be used to charge [the suspects] – the Press Law, the Criminal Code, the Immigration Law or something else.”
Western reporters wanting to work in Indonesia must have a journalist’s visa, but working in Papua and West Papua is even more sensitive, and reporters must gain another, hard-to-get permission form from the foreign affairs department, signed off by the gamut of Indonesian government authorities, including police and military.
Indonesia is highly sensitive about the state of the Papua and West Papua provinces, which have hosted a long-running but low-level separatist insurgency, as well as intractable poverty, social and environmental issues.
Police often argue that journalists are denied permission to enter for their own security.
On a recent trip to Papua, US ambassador to Indonesia Robert Blake drew fresh attention to the situation, suggesting Indonesia would be better off if it lifted its restrictions on foreign journalists reporting on Papua.
Dandois has reported from Somalia, Burma, Kosovo, Darfur and the Gaza Strip. He was arrested and jailed for a month while covering the Tuareg rebellion in northern Niger in 2007. Bourrat is a freelance photographer and videographer. [SydneyMorningHerald]