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The New Orleans Saints quarterback apologised on Thursday for comments he made that he described as "insensitive and completely missed the mark."
Trailblazers - Colin Kaepernick: Taking the knee to demand social justice
He said Wednesday that he "will never agree with anybody disrespecting the flag of the United States of America or our country" while reiterating his objection to NFL players who kneel during the national anthem.
Numerous black athletes, including NBA star LeBron James, expressed outrage at Brees. Several of Brees' New Orleans teammates were among the NFL players who were irate.
Trump, though, said on his Twitter account that he doesn't think Brees needed to issue an apology.
"I am a big fan of Drew Brees. I think he's truly one of the greatest quarterbacks, but he should not have taken back his original stance on honouring our magnificent American Flag. OLD GLORY is to be revered, cherished, and flown high...
"We should be standing up straight and tall, ideally with a salute, or a hand on heart. There are other things you can protest, but not our Great American Flag - NO KNEELING!"
Brees posted an open-letter reply to Trump on his Instagram account on Friday night.
"Through my ongoing conversations with friends, teammates, and leaders in the black community, I realize this is not an issue about the American flag," Brees wrote.
"It has never been. We can no longer use the flag to turn people away or distract them from the real issues that face our black communities.
"We did this back in 2017, and regretfully I brought it back with my comments this week. We must stop talking about the flag and shift our attention to the real issues of systemic racial injustice, economic oppression, police brutality, and judicial & prison reform.
"We are at a critical juncture in our nation's history! If not now, then when?
We as a white community need to listen and learn from the pain and suffering of our black communities. We must acknowledge the problems, identify the solutions, and then put this into action. The black community cannot do it alone. This will require all of us.
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Trump's comments came hours before NFL commissioner Roger Goodell apologised and said that the league was wrong for not listening to players and their concerns about social justice and racism.
Social injustice has been a major source of tension in the NFL since former San Francisco 49ers quarterback Colin Kaepernick began kneeling before games during the 2016 season to bring attention to police brutality. Kaepernick hasn't played in an NFL game since that year.
The NFL's relationship with black players is under scrutiny in the wake of the death of George Floyd in Minneapolis. A group of players requested the NFL take strong action on Thursday in a video directed at Goodell and other NFL officials.
Floyd, a black man, died on May 25 after white Minneapolis police officer Derek Chauvin kneeled on his neck for more than eight minutes in an incident caught on cell phones. Chauvin was charged with second-degree murder, third-degree murder and second-degree manslaughter.
Three other officers - Thomas Lane, J. Alexander Kueng and Tou Thao - were arrested and charged with aiding and abetting both a second-degree murder and a second-degree manslaughter.
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