"That designation will permit the investigation provided by the League's Personal Conduct Policy to run its course and will afford Josh the opportunity to focus on his defense against the charges," the club said in a written statement.
"The Colts sincerely hope this extraordinarily serious matter will be resolved expeditiously and that justice will prevail."
McNary, 26, a reserve linebacker, was charged with rape in a criminal complaint filed Wednesday. He is accused of sexually assaulting a 29-year-old woman in the early morning hours of Dec. 1. According to the complaint, obtained by Sports Illustrated, McNary faces one count each of rape, criminal confinement and battery.
The alleged victim told Indianapolis police that a man took her to an apartment after she had been out drinking with friends following work, according to documents filed with the court.
The man tried to kiss the woman and when she rebuffed his advances, the two fought before he sexually assaulted her, according to the documents. After the incident, the victim told police, she left the residence with the man's cellphone, which was later used to identify McNary.