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6 year oldHis death in 1994 was a trigger of the genocide.
A French inquiry began four years later at the request of relatives of the French crew members who died.
A judge accused Tutsi rebels, led by the current president, Paul Kagame, of the attack; arrest warrants were issued for a number of people close to him.
The charges were dropped on 21 December, a judicial source said on Wednesday.
French prosecutors had recommended in October the charges be dismissed because of insufficient evidence against the suspects.
Lawyers for Habyarimana's widow, Agathe, have told the AFP news agency the plaintiffs in the case would appeal against the decision.
"We have to interpret this decision by French judges as a form of resignation faced with a political context which prosecutors did not know how to fight," lawyer Philippe Meilhac said. "Rwandan authorities have never sought to help bring the truth to light."
The plane carrying Mr Habyarimana was shot down by a missile in April 1994, triggering the Rwandan genocide in which more than 800,000 Tutsis and moderate Hutus died.
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