WASHINGTON — The Education Department will prohibit colleges from granting emergency assistance to undocumented students, even those known as Dreamers who are under federal protection, according to guidance issued to colleges and universities on Tuesday.

Education Secretary Betsy DeVos ordered higher education institutions to dole out more than $6 billion in emergency relief only to students who are eligible for federal financial aid, including U.S. citizens or legal residents. The directive effectively excluded tens of thousands of students who are living in the United States under the Deferred Action for Childhood Arrivals, or DACA, program, an Obama-era policy that protects hundreds of thousands of immigrants brought to the United States illegally as children.

President Trump has moved to end the program, but that effort is awaiting Supreme Court review.

The measure will compound the challenges facing undocumented students, whose families have also been excluded from aid like stimulus checks for individuals and unemployment insurance, said Miriam Feldblum, the executive director of the Presidents’ Alliance on Higher Education and Immigration, which advocates on behalf of immigrant students.

In a recent report, the organization counted 450,000 undocumented students enrolled in the nation’s higher education system, with 87 percent of DACA-eligible students in undergraduate programs, and 13 percent in graduate-level programs.