Brees said on Wednesday he still does not approve of people kneeling and takes offence to the gesture, which he believes is disrespectful to those in the military.
James was then quick to point out that Colin Kaepernick began kneeling in 2016 to protest against police brutality and racial inequality, and his action had nothing to do with those who fight and serve.
"WOW MAN!!" James tweeted, with a facepalm emoji. "Is it still surprising at this point. Sure isn't! You literally still don't understand why Kap was kneeling on one knee?? Has absolute nothing to do with the disrespect of [the flag] and our soldiers [men and women] who keep our land free.
"My father-in-law was one of those men who fought as well for this country. I asked him question about it and thank him all the time for his commitment. He never found Kap peaceful protest offensive because he and I both know what's right is right and what's wrong is wrong!"
James' tweet came in response to remarks Brees made earlier in the day in an interview with Yahoo Finance.
"I will never agree with anybody disrespecting the flag of the United States of America or our country," Brees said when asked about players kneeling.
"Let me just tell what I see or what I feel when the national anthem is played and when I look at the flag of the United States.
"I envision my two grandfathers, who fought for this country during World War II, one in the Army and one in the Marine Corp. Both risking their lives to protect our country and to try to make our country and this world a better place. So every time I stand with my hand over my heart looking at that flag and singing the national anthem, that's what I think about."
The 41-year-old does see a connection between the sacrifices made by those in the military and those fighting for civil rights, but still feels the flag should be respected.
"In many cases, that brings me to tears, thinking about all that has been sacrificed," he said. "Not just those in the military, but for that matter, those throughout the civil rights movements of the '60s, and all that has been endured by so many people up until this point.
"And is everything right with our country right now? No, it is not. 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."
Brees' comments come a day after Blackout Tuesday, a day established to observe, mourn and bring policy change in the wake of the death of George Floyd, the African-American who died on May 25 while in the custody of police in Minneapolis, Minnesota.
Since Floyd's death, people have been protesting in several American cities, calling for an end of police brutality against minorities, and the NFL and the league's teams are addressing ways of supporting and fighting for justice.
Brees called time on his glittering 20-year NFL career on Sunday, with glowing tributes pouring in for the quarterback.
And Pelicans star Williamson, fresh from a 135-115 win over the Los Angeles Clippers, praised someone whose welcoming words have stuck with him.
Williamson was the top pick in the 2019 NBA Draft and received a special message from Brees, who has had a lasting impact on the 20-year-old.
"He's a legend in the game, I think everybody knows that he's a legend," said Williamson, who is 22 years Brees' junior.
"He gave his heart and soul to the game. I know a lot of people are sad to see him go.
"Drew told me I think the truest thing anybody has ever told me, my first game in New Orleans – you love your city, they'll love you right back.
"Whenever new people come and visit, that's the same thing I tell them. That's the kind of influence he's had on me."
Brees is a 13-time Pro Bowler and was MVP in the Saints' Super Bowl win over the Indianapolis Colts in February 2010.
The 42-year-old retires as the all-time leader in passing completions (7,142) and passing yards (80,358).
Ida made landfall on the Louisiana coast as a powerful Category 4 storm, 16 years to the day after Hurricane Katrina devastated the region.
The entire city of New Orleans lost power on Sunday but Gayle Benson, who owns the Saints and the NBA's Pelicans, said in a statement Monday that her teams' facilities suffered only superficial damage.
The Saints relocated operations to the Dallas area over the weekend at the invitation of the Cowboys, and head coach Sean Payton said they will remain there at least through Wednesday.
They are scheduled to host the Green Bay Packers in the regular-season opener on September 12, but Payton told reporters all options are on the table if playing at home is not feasible.
"Obviously we’ll have a plan B," he said. "And, you know, there are a lot of other things probably from a priority standpoint that are more important for our city.
"But that all being said, we fully anticipate starting the regular season with Green Bay and then the question would be where that game's at."
Speaking to reporters before practice on Monday, Payton noted his team's concern over their homes and belongings left behind.
"Left behind are obviously apartments, condominiums, homes. Those are all physical things. Nonetheless, they're still home for so many people," Payton said. "I think to some degree that going out and being able to practice today is going to be good for everyone, because from afar, there’s only so much you can do."
The Saints cancelled their final pre-season game, which was to be played at the Superdome against the Arizona Cardinals on Saturday.
NFL rules mandate teams give players this weekend off from practice, and Payton indicated he did not expect the Saints to be back at their home facility when work resumes next Monday.
Benson said the Federal Emergency Management Agency has accepted the Saints' offer to use their facilities and will stage assistance efforts out of the NFL and NBA teams' practice facility in suburban Metairie.
Benson also said she will donate $1million to a relief fund that will help the region recover from the storm.
"Our team is safe and focussed on preparing for, and winning, the first regular game against the Green Bay Packers," Benson said. "We look forward to returning to New Orleans to continue those preparations as soon as our government leaders say it is safe to do so.
"Fortunately, the Caesars Superdome received only minor damage and will be prepared to host games as soon as the city's infrastructure will allow."
