Speaking to reporters at the AFC coaches' breakfast at the Annual League Meeting in Phoenix on Tuesday, Harbaugh said it was "stupid" and "intellectually lazy" to believe teams are blackballing the former San Francisco 49ers quarterback. "It's more nuanced," he added.
Tuesday evening NFL Commissioner Roger Goodell was also asked about the report.
"I haven't heard that from our clubs in any way that it's an issue," Goodell said. "From my experience in 35 years, is that our clubs make independent evaluations of players. They work hard to try to recruit their teams and if they think a player can help them improve their team, they are going to do that."
Kaepernick's on-field struggles coupled with the off-field notoriety he garnered by taking a knee during the performing of the national anthem before games last season has led many to believe he's locked in a state of free agency purgatory.
Despite the many opinions regarding why Kaepernick remains on the market, Harbaugh is among those who believe the quarterback has a future in the NFL.
"I absolutely think he's going to get signed. I agree with (my brother) Jim (Harbaugh). He can win games for people," said Harbaugh, who added he thinks he can be a starter again.
New Broncos head coach Vance Joseph also doesn't see a big deal with Kaepernick's stance on social issues.
"It does not bother me," Joseph said Tuesday, per the Denver Post. "You have to give the players a right to voice their personal concerns. That doesn't bother me at all. Colin, you would hope he gets evaluated as a quarterback first and then his personal views can be put to the side a little bit."
Joseph went on to say that there are plenty of reasons why Kaepernick and other notable players are still on the free-agent market. Joseph added he isn't surprised the QB is still available.
"It could be numerous issues as far as he's a veteran quarterback, his number could be really high, he doesn't fit a certain offensive philosophy," Joseph said. "It could be numerous things."