Brees has been widely criticized by many fellow athletes, with NBA star Lebron James and Brees' teammate Michael Thomas weighing in.
When asked for his opinion about players kneeling to protest police brutality once the NFL season begins this fall, Brees had said he would "never agree with anybody disrespecting the flag."
"And is everything right with our country right now? No, it's not," Brees said in the interview. "We still have a long way to go. But I think what you do by standing there and showing respect to the flag with your hand over your heart, is it shows unity. It shows that we are all in this together, we can all do better, and that we are all part of the solution."
But in a statement posted on his Instagram account, the 41-year-old Brees said his comments were "insensitive and completely missed the mark on the issues we are facing right now as a country."
"I would like to apologize to my friends, teammates, the City of New Orleans, the black community, NFL community and anyone I hurt with my comments yesterday. In speaking with some of you, it breaks my heart to know the pain I have caused."
A Super Bowl XLIV winner in 2010, Brees said respecting the US national anthem is not just about showing respect to the military, but also to anyone who sacrificed for this country, including those in the civil rights movement.
However following the outcry that surrounded his comments, Brees now acknowledges he takes "full responsibility and accountability."
“They lacked awareness and any type of compassion or empathy. Instead, those words have become divisive and hurtful and have misled people into believing that somehow I am an enemy. This could not be further from the truth, and is not an accurate reflection of my heart or my character,” said Brees.