Kaepernick has denied saying anything "racially derogatory," although he acknowledged that he said something to Houston after throwing an interception against the Bears. Replays show that Kaepernick said something to Houston on the play.
Houston, however, told the Tribune on Monday that the star quarterback was "just saying inappropriate language," including using the N-word and a profanity.
Kaepernick was called for an unsportsmanlike penalty after the play and was fined $11,025 last week. Houston claims he was not insulted by the racial slur, telling the Tribune that it's a "cultural thing."
Kaepernick threw three interceptions in the loss to the Bears. Houston denied hearing Kaepernick using the racial slur when asked on Sept. 14, but Fox Sports, citing NFL referees, reported last week that the quarterback did say the N-word.
After Sunday's loss to the Arizona Cardinals, in the wake of the Fox Sports report and video surfacing of Kaepernick obviously saying something to Houston, the quarterback acknowledged that he talks on the field.
"Yes, I do," he said.
Both Kaepernick and Houston are African-American. The NFL has made a concerted effort this season to police and penalize what it deems inappropriate language on the field.
ESPN.com 49ers reporter Paul Gutierrez contributed to this report.