Sao Paulo police have confirmed to Goal that there has been a complaint made against the player from a Brazilian woman he met in Paris.
The police would not discuss details of the ongoing case, which was filed by the alleged victim on May 31.
Brazilian outlet UOL was the first to report the accusations and claim statements made to authorities are being kept confidential.
Neymar's camp maintains the 27-year-old's innocence, stating that he was the target of a blackmail attempt, while the player's father believes WhatsApp messages sent to his son's phone from the alleged victim would be used to help clear his name.
The forward's national team coach, however, is reserving judgement until all of the facts are made public.
“First of all, I know the importance of the subject, the real extent of it,” Tite told a press conference on Monday.
“The subject is a personal one and there will be time for people to judge the facts. For now, I won't allow myself to judge.
“What I can say is that, in three years together, in our discussions about personal subjects, he was always loyal and truthful.
“I cannot comment or cross any lines – I have a lot of energy to spend on what is essential and important, on preparing the team.
“I understand that you are searching for information to makes judgements upon. I want you to understand that my focus is on preparing for the [friendly] game against Qatar [on June 6].
“If I keep searching and making assumptions it will consume energy and take me away from what I should be focusing on. I want to focus on my work.
“I had two talks with Neymar, but both of them were about personal subjects. We know what we said, the truths we exchanged.
“They are the facts, the captaincy and the importance of him being focused on work.”
Tite was also asked to comment on Neymar's importance to the Brazil national team, to which he replied: “Technically, he is indispensable for Brazil.
“We say he is indispensable, we are not saying he is irreplaceable. He is indispensable, but nobody is irreplaceable.”
But while the coach appears confident that they could cover for the PSG star if needed, the Selecao's general coordinator Edu Gaspar made clear that the Brazil’s football federation, CBF, is assisting Neymar in dealing with the allegations.
“The first thing I did was to hire a lawyer to help us here,” the former Arsenal man, 41, said. “That is the way we are conducting everything.
“We want to have legal advice for him and for the CBF – I even informed his father of that so that we can consolidate all of our information.
“The reason behind the legal advice is to solve the subject as fast as we can so that he can keep his focus on Copa America.”