Police say the incident occurred at a San Francisco hotel last Sunday.
Crabtree has been interviewed by police and has not been detained or arrested.
The 49ers are currently on their way to Atlanta to face the Falcons in the NFC Championship.
49ers General Manager Trent Baalke issued a statement late Friday evening saying, "We are aware of the allegation against Michael and understand that he has fully cooperated with authorities. The 49ers take such matters very seriously. We will have no further comment at this time as the legal process is ongoing. Additional requests for comment should be directed to Michael's attorney."