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The Washington Post reported that when the Arizona Republican stood up and introduced himself, Trump said, "You've been very critical of me."
"Yes, I'm the other senator from Arizona - the one who didn't get captured - and I want to talk to you about statements like that," Flake responded, two Republican officials told the Post.
Flake was referring to Trump's comments from roughly one year ago when he questioned whether Sen. John McCain of Arizona was a war hero because he was captured during the Vietnam War. Trump said he preferred people who weren't captured.
According to the Post, Flake told the Manhattan billionaire that he wants to be able to support him, but is still uncomfortable doing so.
Trump noted he has yet to start attacking Flake and threatened to start. Flake then urged Trump to stop attacking Mexicans, according to the report.
The presumptive Republican nominee predicted Flake would lose his reelection bid, to which Flake shot back that he's not on the ballot until 2018.
Sources told CNN's Manu Raju that Trump also threatened to defeat Flake in an election.
Flake declined to elaborate on the exchange when asked by reporters afterward.
"No, I'll just leave it," he told reporters, adding "my position remains, I want to support the nominee. I really do. I just can't support him given the things that he's said."
Trump also called out Republican Sens. Mark Kirk of Illinois and Ben Sasse of Nebraska, according to the Post. Kirk unendorsed Trump recently while Sasse has been fiercely critical of the real estate magnate.
Trump characterized Kirk as a loser.
"I guess he lit me up," Kirk later told the Post.
AP Photo/Ross D. Franklin
During a recent interview with Business Insider, Flake said anybody who uttered the protectionist rhetoric on trade that Trump has "is not what I'd call a Republican." He also said it's "quite possible" Trump could lose in his state of Arizona, a GOP stronghold, and said he thinks Republicans should consider confirming Judge Merrick Garland to the Supreme Court in October if it looks like Trump is going to lose the election.
"Mr. Trump's problem is not just being dissatisfied with the status quo," he said. "It's that he's gone out and gone after specific groups and organizations. The Mexican judge comments. The Muslim ban, although he seems to be backing off of that. It's just the general statements on too many groups he's going to need to win an election. So I think he's still got to change quite a bit."
He added that "we just don't know" if Trump is capable of change.
"Sometimes he'll walk something back one day and be back with the original policy the next," he said. "So we'll see what holds. He's 70 years old, and it's tough to change. He's made many statements about how he won the primary and why change it. He may, for a time, use more appropriate rhetoric or statements, but I just don't know if that can last. I really don't."