While the groups — some of which received bomb threats — praised law enforcement for making an arrest, they also expressed sadness after learning that authorities believed a 19-year-old Jewish man is behind most of the threats.
"It was heartbreaking to learn that a Jewish man is a prime suspect," Jerry Silverman, president and chief executive of the Jewish Federation of North America, said in a statement.
The stream of bomb threats to U.S. schools and institutions have helped fueled heightened anxiety about anti-Semitism and forced repeated evacuations of Jewish Community Centers, offices, daycares and school buildings.
The Anti-Defamation League said that as of this week, there had been 166 threats made in 38 states as well as three Canadian provinces, a tally that included threatening messages sent to five ADL offices.
"While the details of this crime remain unclear, the impact of this individual's actions is crystal clear: These were acts of anti-Semitism," Jonathan A. Greenblatt, chief executive of the ADL, said in a statement. "These threats targeted Jewish institutions, were calculated to sow fear and anxiety, and put the entire Jewish community on high alert."
The FBI briefed Jewish leaders in the United States on Thursday morning, according to Silverman, who praised "the unprecedented level of time and resources that were committed to this investigation."
Doron Krakow, chief executive of the Jewish Community Center Association of North America, echoed Silverman and said his group was "troubled to learn that the individual suspected of making these threats … is reportedly Jewish."
Krakow described at least one silver lining to the situation.
"Throughout this long running period of concern and disruption that we are hopeful has come to an end, JCCs have had the opportunity to review and assess our security protocols and procedures, and we are confident that JCCs are safer today than ever before," Krakow said in a statement.
The 19-year-old who Israeli police arrested in the case has not been identified by authorities beyond being described as a man with both Israeli and U.S. citizenship.
In at least one case, news of the young man's background prompted more reports of harassment. The Anne Frank Center for Mutual Respect, a nonprofit organization targeting discrimination, said it received anti-Semitic messages on Thursday focusing on the teenager's faith.
Steven Goldstein, the center's executive director, said that the theme of the messages has been this: "See, it's your people, Jews, who were responsible." He also said one message sent to the group told them "a 'white' person was not responsible."
"Such vitriol requires us to respond further: Hate is hate, and our nation had the right to expect this administration to respond to hate with urgency every time," Goldstein said in a statement. He added: "The religion of a suspect doesn't matter. The hateful acts were the same, and the lack of governmental responses along the way were the same."
Goldstein said that it was "immoral and unacceptable" to highlight "the religion of one depraved individual, and use that as a pretext for hate against an entire religion."
The 19-year-old in Israel is the second person arrested in connection with the threats. Earlier this month, law enforcement officials arrested Juan Thompson, 31, a former journalist, and charged him with making at least eight of the threats as part of a campaign to harass a woman.
Much as they did after Thompson's arrest, Jewish groups pointed out that there are still troubling anti-Semitic incidents left unsolved. Greenblatt, the ADL chief, pointed to the vandalism that damaged headstones at Jewish cemeteries in Pennsylvania, Missouri and New York, as well as other episodes.
"No arrests have been made in three cemetery desecrations or a series of other anti-Semitic incidents involving swastika graffiti and hate fliers," Greenblatt said. "JCCs and other institutions should not relax security measures or become less vigilant."
After Thompson's arrest and amid a new wave of threats to Jewish facilities just days later, all 100 U.S. senators signed a letter pleading with the Trump administration to take "swift action with regard to the deeply troubling series of anonymous bomb threats."
President Trump condemned the threats during a speech to Congress this month. He had been criticized earlier for declining to criticize the anti-Semitic threats, and he did so only after receiving intense pushback on the issue.
On Thursday, Goldstein, of the Anne Frank Center, continued to offer additional criticism of the Trump administration, which his group has needled for its response to the threats. "Our organization, like others, had to pull teeth to get a governmental response to the bomb threats and other desecration," he said. "Almost every time, we never got responses."
Trump also unsettled Jewish groups and public officials when he suggested to a gathering of state attorneys general in Washington that the threats might be coming from people seeking to make him or his supporters look bad. Trump also condemned the threatening messages during the meeting, but he then said that sometimes such threats can be made in "the reverse," according to two people who attended.
A White House spokeswoman did not respond to a request for comment about the arrest Thursday.
Matt Zapotosky in Washington and Ruth Eglash in Jerusalem contributed to this report.