Police said Thursday they were following up on a sexual assault claim that involves Kaepernick, 49ers wide receiver Quinton Patton and Seattle Seahawks wide receiver Ricardo Lockette.
Kaepernick wrote on Twitter Friday that media reports are false.
"The charges made in the TMZ story and other stories I've seen are completely wrong," he wrote. "They make things up about me that never happened."
According to the police report, the incident occurred April 1 when a woman went to Lockette's apartment in Miami at 9 p.m. Kaepernick and Patton were there.
The woman, whose name is redacted, reported the incident to police on April 3. She acknowledged a prior sexual history with Kaepernick, the report said.
"I take great pride in who I am and what I do, but I guess sometimes you have to deal with someone who makes things up," Kaepernick wrote.
He also tweeted: "I want to thank all of the people who have shared their encouraging sentiments. I assure you that your faith is not misplaced."
Kaepernick is scheduled to make $1.073 million in the final year of his original four-year contract. A long-term deal could reach an annual average of between $17 million and $20 million per season.
Lockette played in the Super Bowl with the Seahawks and his current contract runs through the 2014 season.