On Monday, Swedish newspapers Aftonbladet and Expressen reported that a rape investigation had been opened following Mbappe's two-day visit to the Nordic capital.
"In response to media reports about a suspected rape in Stockholm, the prosecutor can confirm that a criminal report has been submitted to the police," Sweden's Prosecution Authority said in a statement.
It added that the alleged incident occurred at a hotel on October 10th, but did not name a suspect and said no further information could be shared for the moment.
Expressen on Monday identified Mbappe as the suspect, citing anonymous sources, while Aftonbladet said Tuesday it had also obtained information confirming Mbappe was the suspect.
Expressen said Mbappe was "reasonably suspected" of rape and sexual assault, the lower of two grades of suspicion in the Swedish legal system.
Contacted by AFP on Monday, Mbappe's entourage said it had no knowledge of a legal complaint made against him.
The French international was not selected for his country's latest round of Nations League matches, so visited the Swedish capital with a group of people last Thursday.
According to Aftonbladet, they dined at a restaurant before going to a nightclub. Mbappe and the group left Sweden on Friday.
Aftonbladet said the complaint was filed on Saturday after the alleged victim had sought medical attention.
Expressen reported Tuesday that police had seized some clothing as evidence, saying it consisted of women's underwear, a pair of black trousers and a black top.
On Monday, Mbappe himself claimed in a post on X that there was a link between the Aftonbladet report and his hearing before a French league committee on Tuesday, in his bitter dispute with his former club Paris Saint-Germain over what he says are unpaid wages.
Mbappe claims he is owed 55 million euros (£45.8m million) by the Qatari-owned French champions.
"FAKE NEWS !!!!. It's becoming so predictable, on the eve of the hearing, as if by chance," Mbappe posted.