A charge has been brought against the Paris Saint-Germain and Brazil forward by an unidentified woman following an incident in the French capital on May 15.
Neymar's father insists his son is not guilty of any wrongdoing and claims to "have proof that nothing happened".
The alleged victim took her case to a police station in Sao Paulo that specialises in women's defence on May 31.
The woman claims she met Neymar after exchanging messages on Instagram and a friend of the player arranged for her to travel to France.
It is further alleged that she met the player, who arrived drunk at around 20:00 local time (18:00 GMT), at the Sofitel Paris Arc Du Triomphe where he later had non-consensual sex with her.
In the woman's testimony, she says she returned to Brazil on May 17 but was too emotionally shaken to report the incident until now.
Neymar is currently on international duty with Brazil as the team prepare to host the Copa America.
On Saturday, Neymar Snr told Sao Paulo-based television network Band: "It's a person accusing Neymar, but we have proof that nothing happened.
"Neymar fell into this trap. Now we have to do what we can to show the truth."
Photo Getty Images. Caption: Brazil star Neymar