The Yemen carrier was charged on November 15 in connection with the crash of an Airbus A310 which French authorities have said should not have been allowed to fly, a judicial source said.
All but one of the 142 passengers, who included dozens of French nationals, and 11 crew members, died in the disaster in the Indian Ocean as the craft tried to land in the Comoros capital Moroni.
Only a 14-year-old survived and was rescued from sea.
"It's the end of four-and-a-half years of contempt, repeated hurdles, cowardice and impunity," it said.
Flight IY 626 had left Paris for Sanaa via Marseille. The passengers were transferred to the older plane in the Yemen capital.
The 19-year-old jet had been banned from French airspace. Dominique Bussereau, who was then transport minister, said after the crash that French inspectors had in 2007 found numerous faults with the A310.
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