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The Cockpit Voice Recorder had been located and operations were under way to retrieve it, Ali Abdou Mohamed said.
On Friday, they retrieved the Flight Data Recorder with the help of a specially-equipped French vessel scouring an Indian Ocean zone where the average depth is estimated at 1200 metres.
"The two flight recorders... will be sent in the coming days to the Investigation and Analysis Bureau in Bourget (France) where they will be studied in the presence of the investigations team members," Mohamed said in a statement.
The causes of the crash of the plane, which was carrying mainly passengers of Comoran origin living in France, remain unknown.
Some sources blamed the state of the plane, which did not satisfy European safety regulations, but the investigation has yet to establish this.
The passengers, who were travelling from France to the Comoros, had changed planes in the Yemeni capital Sanaa and boarded the Airbus A310. The plane plunged into the Indian Ocean as it was trying to land in Moroni.
The sole survivor was Bahia Bakari, a 13-year-old girl who lost her mother in the crash and clung to a floating piece of debris for hours before being rescued.
The investigation team is made up of officials from the Comoros, Yemen and France and is headed by the Comoros authorities.
AFP