The suspected pirates were brought to Paris on Wednesday after they were captured by French special forces who chased them in a helicopter as they tried to escape in a four-wheel-drive vehicle.
French troops recovered about $200,000 of the $2m ransom paid, according to French sources.
The French foreign ministry said earlier this week that it was seeking permission from Somalia to put the six men on trial in France.
Somali regional rulers on Thursday demanded compensation for civilian deaths they claim occurred during the military operation and said only two of the six suspects captured were pirates.
Dahir Abdulkadir Ahmed, the governor of the Mugug region where the operation was carried out, said: "There are two people confirmed to be pirates among the six. The other four were khat [a narcotic leaf] traders selling their goods to the pirates."
Somali officials and witnesses said three people were killed during the French operation, but the military in Paris has denied any pirates were killed.