Kaepernick, 49ers wide receiver Quinton Patton and Seattle Seahawks wide receiver Ricardo Lockette were in Lockette's Miami hotel residence with the woman on April 1.
The woman said the four of them were watching a basketball game. She drank mixed alcoholic drinks and smoke marijuana, then went into a bedroom to lie down. She told police Kaepernick came in, kissed her and undressed her, then left.
The woman told police that though she and Kaepernick have had a sexual relationship in the past, they did not have sex.
The other two men peeked in, the woman said, and she kicked them out. She said the next thing she knew, she was waking up in a hospital room with no memory of how she got there.
Police stressed that the report contained only unproven allegations as of Thursday.
"As far as whether there was a crime committed, it's too early to say," said Miami Police spokeswoman Kenia Reyes.
Kaepernick's agent, Scott Smith, did not immediately respond to email and voice mail messages seeking comment. The 49ers and Seahawks issued statements saying they were aware of the incident but declined further comment.
Kaepernick, 26, is one of the NFL's top quarterbacks, leading the 49ers to the Super Bowl after the 2012 season and the NFC championship game this past year. For his three-year career, Kaepernick has thrown for more than 5,000 yards and 31 touchdowns, and he has rushed for 937 yards and another nine touchdowns.
The Associated Press contributed to this report.