"What we're discovering day after day is absolutely unbearable," government spokeswoman Maud Bregeon said on Thursday.
"It raises a profound question: what importance do we give to victims' testimonies? How are investigations conducted?" she told the Europe 1 and Cnews broadcasters.
Lyhanna, 11, went missing on Friday near the village of Fleurance in southwestern France, after she was last seen getting into a man's car.
A 41-year-old father of two children has been detained as the key suspect.
After being shown security camera footage, he admitted giving her a lift but insisted he dropped her off at the swimming pool.
Volunteers on horseback were on Thursday morning helping some 170 police officers still searching for her.
Local prosecutor Clemence Meyer said on Wednesday that several legal complaints had previously been filed against the suspect.
In December 2017, a mother reported that her 17-year-old daughter was in a relationship with the man. The case was dropped in 2018 after the girl said she had consented.
In January 2022, a complaint filed in another part of the country accused him of raping a child younger than 15 in 2020 at his home in southwestern France.
The case was transferred to the local prosecutor but dismissed in 2024 for lack of evidence.
In a third case, on August 22, 2025, the mother of a girl born in 2014 accused him of raping her child between September 2024 and May 2025 at his home, the prosecutor said.
The complaint was first examined in the nearby city of Toulouse, then transferred to the local prosecutor's office, who in January demanded police investigate.
But they had still not questioned him when the 11-year-old disappeared.
"The investigation was still underway when Lyhanna went missing," Meyer said.
She added that a new complaint for alleged rape of a minor had been filed on Wednesday morning but provided no further details.
Interior Minister Laurent Nunez told parliament on Wednesday that he had demanded the justice ministry carry out an administrative probe to identify possible dysfunctions in the handling of these cases.
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