The 49ers are putting off negotiations while police investigate an incident earlier this month at a Miami hotel that may have involved Kaepernick.
The Miami Police Department confirmed last week that Kaepernick, wide receiver Quinton Patton and Seattle Seahawks wide receiver Ricardo Lockette were named in a report filed April 4.
The 49ers and Kaepernick want to get a new deal done before the start of the season, but the two sides are reportedly not close.
Kaepernick enters the final year on his contract that is scheduled to pay him $1,073,000. He is reportedly seeking a long-term deal worth up to $20 million per year.
Kaepernick threw for 3,197 yards last year with 21 touchdowns and eight interceptions. He also rushed for 524 yards with four TDs in leading the 49ers to the NFC championship game.