The girl, who originally told her father that Paty had asked Muslim students to leave the classroom during his lessons, admitted she lied about being present.
The lawyer for the family of Samuel Paty has expressed her anger that a student lied about attending his classes on cartoons of the Prophet Mohammed.
The 47-year-old teacher was assassinated outside the Bois d'Aulne secondary school near Paris on October 16.
Paty had taught students about freedom of expression and blasphemy, which led to complaints and an online campaign against him.
But the 13-year-old girl, who originally told her father that Paty had asked Muslim students to leave the classroom during his lessons, admitted she lied about being present.
The police investigation had revealed in November that the girl "was absent due to illness" during the course given on October 6.
"The situation of the girl was untenable," Virginie Le Roy, the Paty family's lawyer, told RTL radio, "all the elements in the case file prove very early on that she lied."
The student, who has not been officially named, has been charged with "slanderous denunciation".
The girl's lawyer, Mbeko Tabula, told AFP news agency on Monday that the girl had lied "because she felt caught up in a chain of events" and "because her comrades had asked her to be their spokesperson".
"There was a real uneasiness, she felt obliged to add to it to make this message stand out," he said.
But Le Roy had dismissed this statement, saying she was "angry" the student had lied "from the offset".
"This explanation does not satisfy me, it makes me a little angry because the facts are serious, dramatic," she added.
The lawyer has also accused Brahim Chnina, the father of the young girl, of lying. Chnina and an Islamist activist, Abdelhakim Sefrioui, have both been charged with "complicity in murder" and are being held in pre-trial detention.
An 18-year-old radicalised Chechen refugee was shot dead by police after beheading Paty outside the school in Conflans-Sainte-Honorine. He had earlier offered students money for identifying the teacher before attacking him.
Prosecutors have stated that there is a "direct causal link" between the online campaign against Samuel Paty and his murder.
A total of fourteen people have been charged in the case, including six secondary school students, three friends of the assailant, and three young people who were in contact with him on social networks.
The assassination stunned France and led to an outpouring of support at memorial ceremonies and marches around the country.