According to an interview given to Radio Rwanda by Prosecutor general Martin Ngoga, the fugitive could be sent back to Rwanda for trial though there is no extradition treaty between Kigali and Libreville.
He did not mention the exact date of the re-arrest.
The medical doctor was wanted by Interpol following an international arrest warrant issued by the Rwandan judiciary.
According to the prosecution in Rwanda, he allegedly took part in planning the genocide at the National university of Butare (Southern Rwanda) where he was a lecturer.
He is also accused of inciting young Hutus to kill and rape Tutsi women, together with former Minister of Family and women affairs, Pauline Nyiramasuhuko. Nyiramasuhuko is awaiting judgement in her case before the Arusha-based International criminal tribunal for Rwanda (ICTR).
Dr Ndindabahizi had been working at Melen hospital, in the outskirts of Libreville, the capital of Gabon.
© Hirondelle News Agency