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.
In 2017, Brees and his Saints teammates knelt before the national anthem before a game against the Miami Dolphins in London in protest at US President Donald Trump's comments on the NFL and its players. The players stood for the national anthem.
'Always been an ally, never an enemy'
The sporting world has been united in paying its respects to George Floyd after his death in Minnesota, US.
Floyd, a 46-year-old black man, died unarmed after pleading for help as a white police officer knelt on his neck for several minutes while pinning him to the ground.
While protests continue throughout cities across the US, many athletes such as former NBA players Stephen Jackson and Kareem Abdul-Jabbar have called for change.
Brees emphasized that he has "always been ally, never an enemy."
"I stand with the black community in the fight against systemic racial injustice and police brutality and support the creation of real policy change that will make a difference," he said. "I condemn the years of oppression that have taken place throughout our black communities and still exists today.
"I acknowledge that we as Americans, including myself, have not done enough to fight for that equality or to truly understand the struggles and plight of the black community. I recognize that I am part of the solution and can be a leader for the black community in this movement.
"I will never know what it's like to be a black man or raise black children in America but I will work every day to put myself in those shoes and fight for what is right."