However his assistant, Carole Liorthois, has been deported back to France for having overstayed her tourist visa. The pair were arrested in the Indonesian province of West Papua on Wednesday after filming a student rally. Around 150 protesters were asking the Indonesian government for democracy and autonomy.
The Indonesian authorities changed their minds after France's ambassador to Indonesia intervened and sent a letter to the Minister of Human rights who's also in charge of immigration issues.
Presenter: Caroline Lafargue, Radio Australia's French service
Speaker: Baudoin Koenig, French independent TV documentary-maker
LAFARGUE: It's a partial victory for Baudoin Koenig who had to accept a compromise after having acknowledged he had made a mistake with his assistant's visa - a tourist visa which she overstayed one day.
KoeNIG: Today I'm allowed to stay until the 4th of June. It's a compromise. I can continue filming and interviewing - in Jakarta among other places, but of course I'm not allowed to go back to West Papua. I don't accept that. However all the people I am in contact with in West Papua as well as in Jakarta tell me it's a very important decision. It means that there are people here who accept the democratic principle. It's not the mandatory deportation system anymore. And nobody touched my report, my footage wasn't seized. On the whole it's a sign that soon foreigners will be allowed to report in West Papua and I hope that decision will serve as a precedent to improve the situation.
LAFARGUE: The French TV documentary-maker was allowed to stay in Indonesia by the very same Minister of Human Rights who declared two weeks ago that he was considering liberating political prisoners from West Papua. Baudoin Koenig is working on a documentary film exploring Indonesia's history since 1945 and its founding principle: Pancasila- unity in diversity. This led him logically to West Papua- an Indonesian province mainly populated by Melanesian Christians and where a low level pro-independence insurgency has been waged against rule from Jakarta by the Free Papua Movement, the OPM. There were again clashes between Papuan autonomists and Indonesian police earlier this week.
KoeNIG: We have met Neles Tebay, the chairman of the University of Theology in Jayapura, a catholic priest involved in the peace negotiations between West Papuans and Jakarta. And on our way back to the hotel, we've come past a student's demonstration - so we started filming it. There were around 100-150 persons. It was organised by the West Papua National Committee. On the banners, the slogans were: "Respect democracy" and "autonomy for West Papua". This demonstration was very peaceful. And we have been arrested in front of 30 local journalists. I felt aggressively from the two Indonesian policemen who bumped into me until I show them my press card. And then we spent 7 hours in the immigration office.
LAFARGUE: What did they ask you during the seven hours?
KoeNIG: They kept asking the same questions: what are you doing here? Why do you film a demonstration which is against the Indonesian government?
LAFARGUE: Baudoin Koenig spent only six and a half hours reporting in West Papua before being arrested and transferred to Jakarta. The status of foreign journalists in West Papua is not clear. Mr Koenig says the Indonesian immigration was rather ambiguous in the issuing of his journalist visa.
KoeNIG: The director of the immigration service has organised a press conference straight way, in which he has given false information. He has claimed that we didn't have a journalist visa or special arrangements, etc. which isn't true. I've lodged my journalist visa application in February. My papers are in order. But my visa can be read two ways: on my permit, there's a first line that says: the filming will take place in Aceh, Jakarta, Sumatra. Kalimantan, etc., and when it comes to West Papua, there's no mention of Jayapura. But on the other hand, there's a second line that says I can report everywhere in Indonesia except in Poso- in Sulawesi- because there has been a conflict between Christians and Muslims over there.
LAFARGUE: Baudoin Koenig's documentary is to be broadcast on the Franco-German ARTE television network.