TMZ.com claims that the investigation relates to an incident in Miami on April 1 in which a woman said that she spent time drinking and smoking marijuana with 49ers wide receiver Quinton Patton, Seattle Seahawks receiver Ricardo Lockette and Kaepernick, before ending up in the latter's bedroom.
However, no arrests have been made and no charges have been filed against the 26-year-old, who took to Twitter to refute the allegations aimed at him.
"The charges made in the TMZ story and other stories I've seen are completely wrong. They make things up about me that never happened," Kaepernick wrote.
"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. I want to thank all of the people who have shared their encouraging sentiments. I assure you that your faith is not misplaced."
Kaepernick ended last season with 3,197 passing yards, 21 touchdown passes and just eight interceptions while rushing for 524 yards and four touchdowns.