Members of the Detroit Lions take a knee during the playing of the national anthem prior to the start of the game against the Atlanta Falcons at Ford Field on September 24, 2017 in Detroit, Michigan.

NFL owners, in a secret meeting last fall, expressed fears that President Donald Trump would continue pounding the league over players' protests during the national anthem, The New York Times reported Wednesday.

The concerns were aired during a confidential October meeting between players and owners while the controversy over the protests raged in the thick of the NFL season.

"Let's make sure that we keep this confidential," NFL Commissioner Roger Goodell said at the start of the session, the Times reported.

The pregame demonstrations, sparked by former 49ers quarterback Colin Kaepernick protesting police brutality, turned off some right-leaning football fans while the league contended with a decline in ratings.

Trump targeted the protests on several occasions. In a September tweet, the president called on fans to stop going to games as long as the protests continued. He also urged the NFL to "fire or suspend" players who were protesting. During a rally in late September, Trump said the league's business would "go to hell" if it did not change its approach to the protests.

According to the Times, New England Patriots owner Robert Kraft, a Trump friend, was chief among the owners expressing worries about Trump's attacks on the league during the October meeting.

"The problem we have is, we have a president who will use that as fodder to do his mission that I don't feel is in the best interests of America," Kraft said, referring to players' kneeling during "The Star-Spangled Banner," according to the Times. "It's divisive and it's horrible."

Kraft is known as a long-time Democrat but has spoken openly about his close friendship with the Republican president. He visited the real estate magnate at Trump Tower in Manhattan days after Trump won the presidential election.

Representatives for the White House, the NFL and the Patriots did not immediately respond to CNBC's request for comment.

Read the full New York Times report here.