The indictment charges the 29-year-old Swedish citizen Mirsad Bektasevic of Bosnian descent, the 21-year-old Turkish citizen Abdulkadir Cesura and Bosnian citizen Bajro Ikanovic with terrorism.
Their two accomplices, Amir Bajric and Senad Hasanovic, are charged with illegal possession of arms and explosives.
The detention of the three terror suspects in custody has been extended, while Bajric and Hasanovic will be released.
Bektasevic, Cesura and Ikanovic were arrested by the Bosnian federal police in a wider Sarajevo area in mid-October 2005. No more details of the operation have been revealed since then.
The local media speculated that the three had most probably planned an attack on one of the Western countries' embassies in Sarajevo.