The report also says Seattle Seahawks wide receiver Ricardo Lockette and 49ers wide receiver Quinton Patton were there and took part in the incident, which happened at Lockette's Miami luxury apartment.
No arrests have been made in connection with the case, and it remains under investigation.
"As far as whether there was a crime committed, it's too early to say," said police spokeswoman Kenia Reyes.
The woman making the allegations is not named.
According to the police report, obtained by KOMO News, the woman also alleges that she and Kaepernick have had a sexual relationship in the past.
The incident under investigation took place April 1.
According to the report, the woman told police she went to visit Lockette at his Miami apartment and found that Kaepernick and Patton were also there.
They talked for a while and she mixed drinks for them and gave them shots. Then the men told her that she should drink shots and "hit" the bong, which contained marijuana, the woman told police.
After a while, she said she started feeling light-headed and went to a bedroom to lie down. Kaepernick then came into the bedroom, started kissing her and undressed her until she was completely naked, according to the report.
Kaepernick then left the bedroom and said he would be right back. They did not have sex.
Sometime afterward, she said Lockette and Patton opened the door and "peeked" inside while she was still naked, but she told them, "What are you doing? Where is Colin? Get out," according to the police report.
They closed the door and left, and the woman remembers nothing after that until waking up in the hospital bed. She told police she has no idea how she got to the hospital or who took her there.
The report does not say if the woman was injured.
The 49ers organization said in a statement that it is aware of the recent reports about Kaepernick and is in the process of gathering facts.
A Seahawks spokesman issued a statement Thursday saying, "We are aware of the situation, monitoring it closely and will not have any further comment at this time."
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