Donald Trump also acknowledged that Nike has the freedom to make business decisions.
He made the comments in an interview with The Daily Caller's Saagar Enjeti and Vince Coglianese.
"But I think it’s a terrible message that they’re sending and the purpose of them doing it, maybe there’s a reason for them doing it," Trump said. "But I think as far as sending a message, I think it’s a terrible message and a message that shouldn’t be sent. There’s no reason for it."
Trump acknowledged that Nike has the freedom to make business decisions.
"As much as I disagree with the Colin Kaepernick endorsement, in another way — I mean, I wouldn’t have done it," Trump said.
"In another way, it is what this country is all about, that you have certain freedoms to do things that other people think you shouldn’t do, but I personally am on a different side of it," Trump added.
The president also said that Nike is a tenant of his and they pay a lot of rent. However, the NikeTown store he is referring to is closed.
Kaepernick tweeted the ad Monday that featured a picture of his face with the words, "Believe in something, even if it means sacrificing everything. #JustDoIt."
The ad prompted support and criticism across the Internet. Pictures were shared of people destroying Nike logos, while #NikeBoycott began trending as people talked of switching company alliances.
In response, the NFL released a statement Tuesday focusing on social justice.
Nike is the NFL's official uniform sponsor. The partnership was recently extended through 2028.
ESPN's Dan Graziano reported that the NFL was not aware of the Nike ad campaign until it was launched.
The company's chief executive had previously condemned Trump's executive order banning arrivals from Muslim countries.
Kaepernick, the former 49ers quarterback, began kneeling during the national anthem in 2016 as a means of protesting racial inequality and police brutality. Other NFL players, along with numerous other athletes, joined in. During the 2017 season, Trump criticized players who protested and said owners should "fire" NFL players who protest the anthem and referred to them as "son[s] of b------". This led to players protesting as a group.
Meanwhile, Kaepernick hasn't played since the 2016 season. He won the summary judgment phase of his collusion case against the NFL last week.