A Minneapolis nonprofit that works with Somali youth is rejecting nearly $500,000 in federal counter-extremism funding, citing “an unofficial war on Muslim-Americans” launched by President Donald Trump’s administration.

Ka Joog’s announcement was soon echoed across the country by several other nonprofits that had applied for the Homeland Security grant program last year but quickly expressed alarm at signals that the White House would narrow the focus of its counterterrorism strategy to Muslim communities. And Ka Joog’s withdrawal casts doubt on the future of federally funded programming in Minnesota.

A source who has worked closely with the Department of Homeland Security on the Countering Violent Extremism (CVE) program told the Star Tribune that members of Trump’s transition team made clear in a December meeting that they were considering changes to the scope and terminology of the program. The source said CVE grant recipients have also not yet seen any funding under the new program.

The Reuters news agency has reported that the White House might reconfigure the program to focus exclusively on radical Islam, not other forms of terrorism such as racially motivated violence.

Mohamed Farah, Ka Joog’s executive director, said late Wednesday that the nonprofit’s board of directors decided to decline $499,998 in funding — one of the biggest awards announced nationally and easily the largest grant Ka Joog would have received.

A second Minneapolis nonprofit, Heartland Democracy, which ran the nation’s first rehabilitation program for a terrorism defendant, was also set to receive $165,435 from the grant program. It was unclear Thursday whether that group would continue to pursue the funding. Both organizations applied under the focus of “developing resilience,” one of five areas outlined when the department announced the grant in July.

Daniel Koehler, a German scholar who evaluated several Twin Cities terrorism defendants as part of the nation’s first “disengagement and deradicalization” program, said rebranding counterextremism to focus solely on Muslims will “kill off the young CVE field in the States.”

“It will alienate Muslim communities, further deteriorate what is left of trust between Muslims and authorities, play directly into [ISIL] propaganda, push radicalization processes, legitimate far right violence by expressively excluding them from the list [and] raise the total risk of homegrown terrorism in the U.S.,” Koehler told the Star Tribune. “It does everything you shouldn’t do in CVE.”

In a prepared statement, Ka Joog said its board believed that its efforts to bring change have “been hindered by the Trump administration to instill fear, uncertainty and anti-Muslim sentiments.”

Farah is a member of the Somali American Task Force, a Twin Cities organization created as part of a Minnesota pilot project managed by the U.S. attorney’s office. Ka Joog also partnered with the Somali American Parent Association last year to create a family engagement program funded by $85,000 in federal and private money awarded as part of the pilot.

Ka Joog’s decision followed news reports that the Trump administration might recast federal counterextremism efforts to focus solely on terrorism inspired by radical Islamic groups and not also far-right domestic extremists, who have been linked to the slayings of nine black churchgoers in South Carolina and a foiled plot to massacre Somali-Americans in Kansas.

Farah was not alone in expressing dismay at the reports out of Washington. Hodan Hassan, a Twin Cities mental health professional who leads the Somali American Task Force, said Thursday that she was “extremely disappointed and concerned” about the administration’s reported new approach. Hassan helped care for two nieces who were wounded in Kenya during a 2013 Al-Shabab attack on a shopping mall there. She has also led panel discussions with relatives of some of the local Somali men convicted last spring of plotting to join ISIL.

“Rebranding CVE to focus on Muslims alone is a huge setback for all the work we have done,” Hassan said. “When the bigger worry and concern should be white men going shooting folks at their worship space.”

Minneapolis was selected in 2014 as one of three cities to host federal pilot projects aimed at using community engagement to counter terrorism recruitment. U.S. Attorney Andrew Luger changed the name of the Minneapolis pilot to de-emphasize “violent extremism” and emphasize building community resilience.

“For the past three years, I have worked closely with Somali and community leaders to tackle the pervasive threat of terror recruiting,” Luger said in a statement Thursday. “While engaged in this collaborative work with community leaders, I have witnessed firsthand the hurtful and damaging reality of Islamophobia. I look forward to an ongoing relationship with my community partners to address each of these issues as we continue to protect the safety and security of Minnesotans.”

Ka Joog and Heartland Democracy were among 31 grantees announced by Homeland Security a week before Trump’s inauguration. At least one other recipient, the Detroit-area Leaders Advancing and Helping Communities, has said it will also refuse a $500,000 award “given the current political climate and cause for concern.”

Another organization that had applied for federal funds, Life After Hate, which focuses on rehabilitating former neo-Nazis and other domestic extremists, said on Twitter that any new federal focus solely on Muslims would be “a mistake on so many levels.”

The possible pivot by the Trump administration concerns some authorities who have worked on counter-extremism efforts, who worry it would discourage community engagement while playing into the hands of terror propagandists.

Michael German, a former FBI terror investigator and a fellow at the Brennan Center for Justice in New York, has criticized previous CVE efforts under the Obama administration for linking social services with counterterrorism work. But, German said Thursday, doubling down on the Muslim community would only help terrorists obtain their goals by sowing division.

“Unfortunately there are violent people in every community,” German said. “But to target one community as susceptible to violence is both factually wrong and stigmatizing.”

Twitter: @smontemayor