Former 49ers quarterback Trent Dilfer said on Tuesday that Kaepernick's lack of progress this season should be a worry to the franchise, and that he struggles when his first passing option is not considered a viable target.
Kaepernick - who led the team to the Super Bowl in his second season last year - told the San Francisco Chronicle: "I didn't hear what Trent had to say, but he's not in the building with us. So what he's saying really does not affect me at all.
"I'm worried about what this team thinks and what I'm doing in here with my teammates. I think you should ask him if he knows what my progression is first before he says that."
The 26-year-old dropped back on passing plays on 28 occasions during last Sunday's defeat to the Carolina Panthers.
The 6-3 49ers sit in second spot in the NFC West.