Trump made the remarks after touring the newly opened National Museum of African American History and Culture.
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"This tour was a meaningful reminder of why we have to fight bigotry, intolerance and hatred in all of its very ugly forms," Trump said.
On Monday, 11 Jewish community centers across the country received phoned-in bomb threats, according to the JCC Association of North America. Like three waves of similar calls in January, Monday's threats proved to be hoaxes, the association said in a statement. All of the affected centers have returned to normal operations.
"The anti-Semitic threats targeting our Jewish community and community centers are horrible and are painful and a very sad reminder of the work that still must be done to root out hate and prejudice and evil," Trump said. He did not outline what that might include.
The president's comments marked the first time he had directly addressed recent incidents of anti-Semitism and followed a more general White House denouncement of "hatred and hate-motivated violence."
That statement, earlier Tuesday, did not mention the community center incidents or Jews. Trump "has made it abundantly clear that these actions are unacceptable," that statement said.
The FBI said it is joining with the Justice Department's Civil Rights Division to investigate "possible civil rights violations in connection with threats."
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On Monday, Trump's daughter Ivanka Trump wrote on Twitter, "We must protect our houses of worship & religious centers," and used the hashtag #JCC. She converted to Judaism ahead of her 2009 marriage to Jared Kushner. She joined her father at the African American museum tour.
Throughout his campaign, Trump was criticized for what some saw as belated and inadequately forceful denunciations of hateful rhetoric by supporters.
Early Tuesday, former presidential rival Hillary Clinton pressured Trump to speak out. "JCC threats, cemetery desecration & online attacks are so troubling & they need to be stopped. Everyone must speak out, starting w/ POTUS," she said on Twitter.
The White House was also criticized by Jewish groups last month after issuing an International Holocaust Remembrance Day statement that did not mention Jews.
Trump's latest remarks came as he paid a visit to the National Museum of African American History and Culture with a group that included Ben Carson, his rival-turned-Secretary of Housing and Urban Development.
The museum includes an exhibit dedicated to Carson's rise from poverty to prominent pediatric neurosurgeon, which the group stopped to admire and pose for photos in front of.
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"Honestly, it's fantastic," Trump said during the tour. "I've learned and I've seen and they've done an incredible job."
Trump's wife Melania Trump visited the museum last week with Sara Netanyahu, wife of the Israeli prime minister.
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Associated Press writer Julie Bykowicz contributed to this report from Washington. AP writer Patrick Mairs contributed from Philadelphia.
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