Jean-Michel Lambert was found dead late Tuesday in his apartment in Le Mans with a plastic bag over his head, according to the local prosecutor. He was 65.
"There were no signs of violence," said the prosecutor, Fabrice Belargent, adding that no note had been left behind.
A source close to the case said there was "little reason to doubt" a suicide.
Lambert was 32 years old and the only investigating magistrate in the district when he took up -- and critics say bungled -- the investigation of the murder of Gregory Villemin.
His murder led to one of France's most notorious post-war murder mysteries, as police sought to untangle a web of family hatred and local jealousies.
But last month, nearly 33 years after the murder, police arrested Marcel Jacob, an uncle of Gregory's father, and Jacob's wife in the Vosges mountains of eastern France.
A neighbour alerted police after discovering Lambert's body Tuesday, media reports said. There were no signs of a break-in.
"I criticise the conclusions he drew from his investigation but I won't ever criticise the man," he added.
Lambert is remembered for his willingness to speak to the press during his investigation.
In particular, he revealed the accusations of Murielle Bolle, a 15-year-old girl, against her brother-in-law, Bernard Laroche.
Laroche, a cousin of the child's father, was charged with the murder a month after the boy's death, based on her evidence.
Investigators involved in the case today want in particular to find out why Bolle went back on her original accusations, and last month she herself was placed under investigation in the case.
Bolle's lawyer, Jean-Paul Teissonniere, told AFP he was concerned by Lambert's death. He had intended to call him as a witness.
At one point Lambert even charged Gregory's mother with his murder, but the country's supreme court finally dismissed the charges.
His work contradicted Lambert's early theories, and the latest investigation is based on Simon's conclusions.
In a 2014 memoir, "How many injustices am I guilty of?" Lambert acknowledged that his early work had not been perfect.
"When I started my career as an investigating judge ... I suffered for some time from a feeling of superiority," he said.
But in comments to AFP the same year, he said that whatever went wrong in the Gregory affair was not just his responsibility but that of the justice system as a whole.
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