Justice Minister Gérald Darmanin on Wednesday ordered the internal investigation to determine whether there had been any judicial "failures", according to a letter of assignment seen by AFP on Friday.
Results are expected by the end of July.
Dominique Pelicot, 72, was sentenced to 20 years in jail for raping and organising for dozens of men to rape his then wife Gisèle Pelicot from 2011 to 2020 while she was drugged.
The case, which shocked the world and turned his ex-wife into a feminist hero, was uncovered after police caught him filming up women's skirts at a supermarket in 2020.
During the months-long trial, it emerged that Dominique Pelicot had also been arrested a decade earlier in a shopping centre for the same offence and that police had taken a sample of his DNA.
Investigators identified a "link to an unknown sample collected in a previous probe opened after an attempted rape" in 1999, as well as a connection to a second case of rape and murder dating back to 1991, the letter said.
Despite this, they do not appear to have further pursued these leads in 2010.
Dominique Pelicot was only charged in both cases in January.
He has admitted to the 1999 attempted rape, but denied involvement in the 1991 rape and murder case.
Similarities in the two cases include both the victims having been young real estate agents aged 23, who were visited by a man under a false name to view an apartment.
In a separate case, Dominique Pelicot's daughter, Caroline Darian, in March filed a legal complaint accusing her father of also drugging and sexually abusing her.
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