Trump, the Republican front-runner for the November 2016 presidential election, has proposed banning Muslims from entering the United States. On Tuesday, he compared his plan to the World War Two detainment of Japanese-Americans.
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Asked about Trump's remarks, Pentagon spokesman Peter Cook said Muslims serve in the US armed forces and that America's war strategy to combat Islamic State hinged on support from Muslim countries.
"Anything that bolsters ISIL's narrative and pits the United States against the Muslim faith is certainly not only contrary to our values but contrary to our national security," Cook told a news briefing, using an acronym for Islamic State.
Cook did not mention Trump by name and said he did not want to wade into domestic political matters. The Pentagon is helping local forces battle Islamic State and other extremists in Iraq, Syria, Afghanistan and elsewhere.
US Homeland Security Secretary Jeh Johnson said Trump's proposal could thwart US efforts to connect with the Muslim community, and Secretary of State John Kerry said his ideas were not constructive.
The Pentagon counts thousands of service members who self-identify as Muslims.
Data released by the Defense Department showed that 3,817 active-duty members and 2,079 members of the National Guard and reserve identified their faith as "Islam."
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The identifications are voluntary and there could be more members of the Muslim faith.
"There are, again, men and women in uniform today of the Muslim faith who are serving this country patriotically," Cook said. "Anything that tries to challenge American values on this would be certainly something of concern."
Within the active-duty US military, some 1,928 soldiers identify themselves as Muslim, along with 879 sailors, 424 Marines and 595 members of the Air Force.
Still, Muslims represent a fraction of the overall 1.3 million active-duty members of the US military and 826,106 members of the guard and reserve.
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According to various estimates, about 3 million Muslims live in the United States, making up just less than 1 percent of the US population.
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