"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.
I apologize for misspeaking my true sentiments. To clarify, I support Colin's motivation. It's his method of action that I take exception to— Coach Harbaugh (@CoachJim4UM) August 29, 2016
Kaepernick remained seated while the national anthem played prior to the 49ers' preseason game Friday 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."
"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.
Cleveland Browns Hall of Fame running back Jim Brown said he did not necessarily agree with the method but that he stands in support of Kaepernick's readiness to keep fighting for what he believes in.
"I listened to him, and he makes all the sense in the world," Brown said in an interview on "NFL Total Access." "He's within his rights and he's telling the truth as he sees it. I am with him 100 percent."
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."
Rick Monday, who prevented two protesters from setting a U.S. flag on fire in left-center field of Dodger Stadium while he was an outfielder for the Chicago Cubs in 1976, said he was "shocked" by Kaepernick's protest.
"The problem I have is whether he's actually giving attention to himself, or is it the issues?" Monday, who spent six years in the U.S. Marine Corps Reserve, told USA Today Sports.
"It's freedom of speech," Monday said, "but the flag itself, I look at it from a positive standpoint. I look at it from the standpoint where I heard today from one of the moms who lost their son. It's like Barbaralee [Monday's wife] says, 'We drape the caskets of our fallen warriors with the flag, and it's presented to the family with the words, from a grateful nation.'
"So how grateful are we if we do not respect the very people that have given? They gave the ultimate, protecting the rights and freedoms the flag represents."
American tennis player John Isner also weighed in on the debate when asked about Kaepernick after winning a first-round match at the US 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 quarterback.
"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."
Oakland Raiders fullback Marcel Reece thought Kaepernick was "misunderstood" and brought up the late Muhammad Ali as an example of why critics should not be too harsh on Kaepernick's message, even if they disagree with how he presented it.
"Muhammad Ali, who stood for so many things and was criticized for not wanting to go to [the Vietnam] war, turned into this legend and this civil rights activist and this immense figure, not only in black America but America, period," Reece told ESPN on Monday. "[Kaepernick] is trying to use his platform to stand up for people who can't necessarily stand up for themselves.
"But, at the same time, I think personally you have to have a little balance in your take on everything."
Pittsburgh 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 writers Jamison Hensley and Paul Gutierrez and The Associated Press contributed to this report.