"I acknowledge his right to do that. I don't respect the motivation or the action," said Harbaugh, who coached Kaepernick with the San Francisco 49ers.
Harbaugh looked to clarify his comments in a tweet later Monday.
Kaepernick remained seated this weekend while the national anthem played prior to the 49ers' preseason game against the Green Bay Packers. After the game, he told reporters he sat because he didn't want to show pride in a country that oppresses people of color.
"To me, this is bigger than football, and it would be selfish on my part to look the other way," Kaepernick told reporters. "There are bodies in the street and people getting paid leave and getting away with murder."
Harbaugh coached Kaepernick in San Francisco for four seasons before leaving for the Michigan job last year. Harbaugh benched Alex Smith in favor of Kaepernick in 2012, giving Kaepernick an opportunity to rise to a higher profile in the NFL.
Harbaugh's brother -- Baltimore Ravens coach John Harbaugh -- said Monday that he respected Kaepernick's right to protest, even if he doesn't agree with how he's doing it.
"Voltaire so eloquently stated, 'I may not agree with what you say, but I'll defend it until death your right to say it,'" John Harbaugh said. "That's a principle that our country is founded on. I don't think you cannot deny someone the right to speak out or mock or make fun or belittle anybody else's opinion."
John Harbaugh, however, said it's a fine line between standing up for what you believe in and not becoming a distraction to the team. He tells his players that you have to make sure you believe what you say publicly because you have to own it.
"You respect our team, our organization and the other players," John Harbaugh said. "You respect the mission that we're on and what we're trying to accomplish. None of us ever want us to detract or disrespect the efforts of all the other players on the football team. That's the balance that all of us have to strike when we speak out about something like that."
The Harbaughs were just a couple of the many football voices to weigh in Monday on Kaepernick's protest. Miami Dolphins defensive tackle Ndamukong Suh said he understood where Kaepernick was coming from.
"I think it's an individual choice," Suh said before practice Monday. "At the same time, I think a lot of [us] as leaders, especially with young kids, is to make a good, proper announcement if you feel the need to. I think that's what he's doing. I support him in that and for me, I just have to move forward and go with the punches."
Green Bay Packers coach Mike McCarthy called the protest an "educational opportunity," while Detroit Lions coach Jim Caldwell said he would not put a mandate on his players to stand during the anthem.
New Orleans Saints quarterback Drew Brees? voiced his displeasure with the protest and said he believes standing for the anthem is a way for players to give thanks to military members who have "sacrificed so much for that flag throughout history."
"I wholeheartedly disagree," Brees told ESPN's Mike Triplett on Monday. "Not that he wants to speak out about a very important issue. No, he can speak out about a very important issue. But there's plenty of other ways that you can do that in a peaceful manner that doesn't involve being disrespectful to the American flag."
Brees said he felt compelled to speak out because he has always been a passionate supporter of the military and feels the American flag is the "one thing that's sacred."
"Sitting down for that, that is a blatant disrespect of the freedoms that that gives you," Brees said. "Like, it's an oxymoron that you're sitting down, disrespecting that flag that has given you the freedom to speak out."
Republican presidential nominee Donald Trump challenged Kaepernick's protest as a "terrible thing."
"Maybe he should find a country that works better for him," Trump told The Dori Monson Show on 97.3 KIRO FM in Seattle. "Let him try. It won't happen."
American tennis player John Isner also weighed in on the debate after being asked about Kaepernick after winning a first-round match at the U.S. Open on Monday.
"I thought that was pathetic from him,'' Isner responded. "The cause he was going for, fine by me -- but don't do it in that fashion. He could have found some other ways to present his voice there.''
Isner ended his answer -- and his news conference -- by declaring: "I'm a big Blaine Gabbert fan now,'' a reference to another 49ers QB.
"There is some depth and some truth into what he was doing," Sherman said. "I think he could have picked a better platform and a better way to do it, but every day they say athletes are so robotic and do everything by the book. And then when somebody takes a stand like that, he gets his head chopped off."
Steelers?left tackle Alejandro Villanueva, who played at Army and served in Afghanistan before forging a job in the NFL, said he agrees that the U.S. "is not perfect'' but insists it is the best country and he is unsure how he would react if one of his teammates sat down for the anthem.
"I just know that I am very thankful to be an American. I will stand very proudly, and I will sing every single line in the national anthem every single time I hear it,'' Villanueva said. "I will stop whatever I am doing, because I recognize that I have to be very thankful to be in this country.''
ESPN staff writer Jamison Hensley and The Associated Press contributed to this report.