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 in 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."
The 49ers arrived at the Ritz-Carlton in downtown Atlanta around 11:15 p.m. ET. Crabtree was on the first bus. He stood up and then he sat down as 10 to 15 other 49ers players got off the bus, almost trying to distract the media, trying to make it difficult for them to shoot video of anyone getting off the bus. Then when Crabtree walked off the bus, he was quickly escorted by a security person off the bus and into the hotel.
A lot of his teammates may not have known about the situation due to the timing of the statement by Baalke.
This subject most likely won't be talked about on the team as they prepare for the championship game on Sunday, but it may be a distraction for Crabtree.
Some fans ABC7 News spoke with Friday night are surprised by these allegations.