"Twelve bodies that have been stored at the morgue are Japanese," the source told AFP after the government in Tokyo said it had no confirmation of the fate of 10 of its nationals who remain unaccounted for.
The source gave no details about the nationalities of other victims of the hostage attack by heavily armed men at the remote gas complex, saying only: "We are in the process of gathering information."
In Tokyo, a Japanese engineering firm said that 10 of its Japanese and seven of its foreign workers remained unaccounted for.
Two Algerian survivors of the hostage crisis employed by the Japanese firm JGC told AFP nine Japanese workers were killed during the four-day siege, which ended on Saturday with a bloody final assault by Algerian special forces.
A special government plane was due to leave Algeria for Tokyo on Sunday evening to repatriate seven other Japanese employees of JGC who survived the ordeal.