Trump spoke after players of America's most popular sport took a defiant stand, in the largest such demonstration since former San Francisco 49ers quarterback Colin Kaepernick started the protests in 2016.
Trump has ignited a firestorm of criticism after comments on Friday in which he described NFL players who chose to take a knee through renditions of "The Star-Spangled Banner" as "sons of bitches" who should be fired.
The US leader doubled down on those remarks early Sunday, urging fans to boycott the NFL as long as the protests continued, and demanding team owners to "fire or suspend" players who take a knee.
Before boarding Air Force One in New Jersey to head back to Washington, Trump declined to repeat the comments he posted on Twitter earlier, saying instead the protests were "disrespectful to our country and very disrespectful to our flag."
He said "the owners should do something about it."
"When you get on your knee and you don't respect the American flag or the anthem that is not being treated with respect... This has nothing to do with race or anything else. This has to do with respect for our country, and respect for our flag."
Protests during games on Sunday were the latest twist in a bitter war of words between Trump and US professional sports.
On Saturday, he had also drawn a furious backlash from NBA stars after stating on Twitter that the champion Golden State Warriors and star Stephen Curry would not be invited to attend a White House reception.
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