WASHINGTON — The Education Department will prohibit colleges from granting emergency assistance to students who entered the country illegally, even those known as Dreamers who are under federal protection, according to guidance issued to colleges and universities 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 Donald Trump has moved to end the program, but that effort is awaiting Supreme Court review.

The measure will compound the challenges facing these students, whose families have also been excluded from aid like stimulus checks for individuals and unemployment insurance, said Miriam Feldblum, 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 students living in the U.S. illegally who are enrolled in the nation’s higher education system, with 87% of DACA-eligible students in undergraduate programs and 13% in graduate-level programs.

In a recent survey of more than 1,600 students, conducted by the organization TheDream. US, a national scholarship organization for Dreamers, 80% of those working have experienced income loss, said Candy Marshall, the group’s president. Sixty-five percent reported that they needed help with rent and utilities, and 48% said that of food.

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“This is not simply saying undocumented students shouldn’t get things that other students don’t get,” Feldblum said. “This was a choice. This was going to be a core lifeline.”

The funding is part of $12.6 billion allocated directly to colleges and universities under Congress’ $2 trillion coronavirus stabilization law to help them recoup financial damage caused by the pandemic. Half of those funds are supposed to go directly to students affected by campus closures. In the coming weeks, schools are expected to award emergency relief grants to students to pay for expenses like food, housing, child care and technology.

The stimulus law, called the Coronavirus Aid, Relief and Economic Security Act, or CARES Act, directs the secretary to distribute the stimulus funding to colleges in the same manner the department distributes other financial aid. ​But it ​did not explicitly define which students are eligible. Students in the country illegally do not qualify for federal financial aid funds, but ​the emergency grants do not fall under that category.

In a statement, Angela L. Morabito, a department spokeswoman, defended its decision.

“The CARES Act makes clear that this taxpayer-funded relief fund should be targeted to U.S. citizens, which is consistently echoed throughout the law,” she said.

Higher education groups were not surprised that the Trump administration targeted immigrants who are living here illegally but said DeVos’ messaging had been inconsistent.

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In a letter announcing the grants, DeVos said the law “provides institutions with significant discretion on how to award this emergency assistance to students” and “the only statutory requirement is that the funds be used to cover expenses related to the disruption of campus operations due to coronavirus.”

“This means that each institution may develop its own system and process for determining how to allocate these funds, which may include distributing the funds to all students or only to students who demonstrate significant need,” she wrote.

The new guidance has caused “head-snapping uncertainty on college campuses,” said Terry Hartle, a senior vice president at the American Council on Education.

“We fear that campuses will be in the position to only give money to people already getting financial aid, using a complicated, time-consuming process that is completely inconsistent with emergency grants,” Hartle said.

He added that the decision was clearly made by the department. “Congress had nothing to do with it,” he said. “The department has to own it.”

Justin Draeger, president of the National Association of Student Financial Aid Administrators, said the department’s method to exclude DACA and students in the country illegally by enforcing federal aid eligibility rules created obstacles for large swaths of other students, including international students and citizens who do not fill out a Free Application for Federal Student Aid, or FAFSA.

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The department’s interpretation would require that schools verify eligibility requirements like whether students have minor drug convictions, have defaulted on student loans or, for men, have not registered with the Selective Service.

Draeger said he feared schools would default to prioritizing students who had federal financial aid applications on file rather than those who needed the assistance most.

“Schools are feeling frustrated that the department has overreached, and they’re cautious about moving forward at this point,” Draeger said.

Wesley Whistle, a senior adviser for policy and strategy at think tank New America, said the measure was consistent with the Trump administration’s track record, especially since relief was being directed to for-profit colleges, which the administration has treated favorably.

“It’s crazy that they’re willing to give away money to for-profits, including those that have had settlements for predatory practices, but they want to make it harder for black and brown students to get it,” he said. “We’re in a pandemic, for Pete’s sake.”