While not officially disclosing the details of the disciplinary measures, sources told Reuters the striker will be fined and removed from the rest of the group for an indeterminate period of time.
"Valencia CF wishes to reiterate its firm condemnation of any type of violence in any of its manifestations, whilst respecting the presumption of innocence that our legal system promulgates. It is up to the courts to determine the timing and the actions regarding the alleged facts for which Rafa Mir is being investigated," Valencia said in a statement.
"However, as far as the Club is concerned... Valencia CF has analysed the situation from the point of view of the sanctioning regime applicable to professional football and has decided to take disciplinary measures.
"Specifically, the Club will proceed to open disciplinary proceedings against Rafa Mir as it understands that his way of proceeding, in his time off, indisputably affects the professional performance expected of him as a player of this Club; damaging, furthermore, the confidence that our fans have in all its players."
Earlier on Monday, Mir categorically denied having committed sexual assault and apologised for "failing to comply, even on a day off, with the rigorous timetable expected of a professional and even more so after a start to the season that fell short of our expectations".
Mir, who has also played for Wolverhampton Wanderers and Sevilla, was arrested last week after a woman filed a complaint against him, and he testified before a judge on Wednesday.
The judge who ordered his conditional release will now lead an investigation to establish whether there is enough evidence for Mir to stand trial or if the case should be dropped.
Mir will have to appear in court regularly and is not allowed to leave the country.