WASHINGTON — President Trump on Thursday disavowed the “send her back” chant that broke out at his re-election rally Wednesday night when he railed against a Somali-born congresswoman, as Republicans in Congress rushed to distance themselves and their party from the ugly refrain.

Mr. Trump said he was “not happy” with the chant, directed at Representative Ilhan Omar of Minnesota, a hijab-wearing freshman Democrat whom the president has singled out repeatedly for verbal excoriation. On Thursday he claimed that he had tried to cut off the chant, an assertion contradicted by video of the event. Asked why he did not stop it, Mr. Trump said, “I think I did — I started speaking very quickly.”

In fact, as the crowd roared “send her back,” Mr. Trump looked around silently and paused as the scene unfolded in front of him, doing nothing to halt the chorus.

“I was not happy with it,” Mr. Trump said on Thursday at the White House. “I disagree with it.”

“I didn’t say that,” he added. “They did.”

Mr. Trump’s effort to dissociate himself from his own supporters reflected the misgivings of his allies, who have flooded the upper echelons of his team with expressions of concern in the wake of a rally that veered into ugly nativist territory. They warned privately that the president was on dangerous ground, according to people briefed on the conversations.

Among them were House Republican leaders, who pleaded with Vice President Mike Pence on Thursday morning to separate the party from the message embraced by the crowd in Greenville, N.C.

“That does not need to be our campaign call, like we did the ‘lock her up’ last time,” said Representative Mark Walker, Republican of North Carolina, a top official in the party’s messaging arm, who attended the rally and tweeted hours later that he had “struggled” with the chant. “We cannot be defined by this.”

Still, while they denounced the chant, Republican leaders declined to criticize Mr. Trump.

Congressional Republicans have struggled all week to respond to Mr. Trump’s attacks on Ms. Omar, one of the first two Muslim women elected to the House, and three other Democratic congresswomen of color who he tweeted over the weekend should “go back” to their countries. Now they must contend with the nativist fervor of his supporters as captured in the frenzied moment in North Carolina, with a rageful refrain that they worry could further damage their party’s brand.

“Those chants have no place in our party or our country,” Representative Kevin McCarthy of California, the Republican leader, told reporters.

Those were almost the exact words used by Representative Tom Emmer of Minnesota, the chairman of the House Republican campaign arm, earlier Thursday, when he repudiated the chant, but insisted that the Twitter posts that inspired the slogan had been mere mistakes of wording.

“There’s no place for that kind of talk,” Mr. Emmer said at a breakfast with reporters in Washington where he was asked about the chant. “I don’t agree with that.”

“There’s not a racist bone in the president’s body,” he added, referring to Mr. Trump’s tweets. “What he was trying to say, he said wrong.”

Still, Mr. Trump’s inner circle seemed to appreciate the gravity of the scene on Wednesday night and urge him to quickly repudiate the chant. Ivanka Trump, his daughter and senior adviser, talked to the president about it on Thursday morning, the people familiar with the discussions said, speaking on condition of anonymity because they were not authorized to divulge them.

[The painful roots of Mr. Trump’s “go back” comment.”]

Ms. Omar, a Somalian refugee, called Mr. Trump a “fascist,” but said there was nothing new about his behavior or the response of his supporters. She cited his years of false claims that Barack Obama was not born in the United States.

CreditAnna Moneymaker/The New York Times

“He does that every single day, and it’s no different,” Ms. Omar said at the Capitol. “What I’m going to be busy doing is uplifting people, and making sure they understand: Here in this country we are all Americans, we are all welcome, irregardless of what he says.”

Even the House’s chaplain, the Rev. Patrick J. Conroy, could not help but join the fray. He opened the House’s session on Thursday with a pointed prayer: “This has been a difficult and contentious week in which darker spirits seem to have been at play in the people’s house. In your most holy name, I now cast out all spirits of darkness from this chamber, spirits not from you.”

Mr. Walker said he had raised the issue with Mr. Pence at a breakfast on Thursday, saying the chant was “something that we want to address early,” before it became a staple of the president’s arena-style rallies. “We felt like this was going to be part of our discussion, to make sure that we are not defined by that.”

The repudiation of the chant was widespread, but it was anything but clear whether the condemnations would have any impact on the president’s crowds in the future.

“The ‘send her back’ chants were wrong, vile, and don’t reflect who we are as Americans,” Matt Brooks, the executive director of the Republican Jewish Coalition, wrote on Twitter. “I strongly oppose @IlhanMN views and policies but those chants have no place in our society.”

At least one civil rights group, Muslim Advocates, said Wednesday that Mr. Trump’s tweets and language were endangering the lives of Ms. Omar and Representative Rashida Tlaib, Democrat of Michigan, the other Muslim woman elected to Congress in November.

“The president’s open, calculated, anti-Muslim bigotry is something we expect to see much more of throughout the 2020 campaign,” Madihha Ahussain, the group’s special counsel for anti-Muslim bigotry, said in a statement. “All Americans, including all Democrats and Republicans, should unequivocally and immediately disavow this hatred.”

Mr. Trump tweets on Sunday targeted Ms. Omar and Ms. Tlaib, as well as Representatives Alexandria Ocasio-Cortez of New York and Ayanna S. Pressley of Massachusetts. All of them are American citizens.

“This president is evolving, as predicted, deeper into the rhetoric of racism, which evolves into violence,” Ms. Ocasio-Cortez said Thursday. She said she was worried for her safety and that House Democrats were discussing how to address security concerns that have stemmed from Mr. Trump’s targeting of their members.

Ms. Omar did not express concern for her own safety, but she worried about fellow Muslim immigrants.

“What I am scared for is the safety of people who share my identity,” said Ms. Omar, who has stood out visually in Congress with colorful head coverings that make her unique in the Capitol. “When you have a president who clearly thinks someone like me should go back, the message that he is sending is not for me, it is for every single person who shares my identity.”

Mr. Emmer tried to minimize the president’s initial remarks.

“What he was trying to say is that if you don’t appreciate this country, you don’t have to be here,” Mr. Emmer said. He quoted a constituent who told him that Ms. Omar’s statements led people to believe that she hated America, adding, “How about a little gratitude with that attitude?”

The latest criticism of Mr. Trump’s language comes two days after the House took the remarkable step of passing a resolution condemning his tweets and asserting that they were “racist comments that legitimized and increased hatred of new Americans and people of color.” Only four Republicans voted yes. All others, including the House leaders who expressed concern to Mr. Pence on Thursday about the chant, voted “no.”

Hours before the chant broke out at the president’s re-election rally, the House killed an attempt by Representative Al Green, Democrat of Texas, to impeach Mr. Trump for the statements, which he said had sullied the office of the president.

But on Thursday morning, his race- and ethnicity-based insults were cited by Representative Peter Welch of Vermont, the latest Democrat to call for impeachment, as one piece of evidence that his presidency has, “wrought an unprecedented and unrelenting assault on the pillars and guardrails of our democracy.”

“Instead of embracing the fundamental responsibility of every American president to unite our country, this president has unleashed a torrent of attacks on fellow citizens based on their race, gender, religion and ethnic origin,” Mr. Welch said in a statement.

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