President Trump took direct aim at elite universities this spring, prompting an outcry over the choking off of billions of dollars in federal research funding from top-tier institutions.

But far from historic campuses in Cambridge and Manhattan, a White House-instigated financial drama was playing out at institutions like Nebraska Indian Community College. The dollar figures were much smaller, but the stakes for students and faculty members were about as high.

The campus sits along a two-lane highway near the Iowa border and is one of 37 tribal colleges and universities that rely almost entirely on federal money to operate — a funding system built on decades of laws and treaties. But when the administration proposed cutting the Bureau of Indian Education’s budget for the dozens of institutions to $22 million, from $183 million, many of them found their futures very much in doubt.

N.I.C.C., which serves several hundred degree-seeking students, had one of tribal education’s most enviable reserve funds, valued at about $5 million. But its president, Michael Oltrogge, figured the college could stay open for only a year if the federal budget cut passed. Just up the road, Manoj Patil thought the institution he leads, Little Priest Tribal College, could last maybe six months more.

Two congressional committees quietly rebuffed the proposal last month, signaling that the cut was unlikely to be included in any budget that clears Capitol Hill this year. The episode, though, underscored the fragile finances of America’s tribal colleges, which have never received as much federal funding as they are promised by law. It also showed how the Trump era’s budget brinkmanship could unleash dread and uncertainty on the country’s smallest campuses.

“There’s billions and billions of dollars of money out there, and you’re looking at the smallest speck, and you’re taking that by 83 percent?” Mr. Patil, whose college draws the vast majority of its funding from the federal government, asked incredulously.

Mr. Patil, who is also the treasurer of the American Indian Higher Education Consortium’s board, estimated that the budget proposal would have left no more than a half dozen tribal colleges open.

“Most of us don’t have much of anything,” Dr. Oltrogge said over a fry bread lunch at N.I.C.C., which has relied on federal support throughout its 52-year history. He added, “I keep trying to remind everybody: Don’t spend all of your money, because we don’t know what they’re going to do, ever.”

The Bureau of Indian Education uses its budget to underwrite 35 colleges that are tribally controlled and to operate directly Haskell Indian Nations University in Kansas and Southwestern Indian Polytechnic Institute in New Mexico.

But federal funding for tribal education is often inconsistent, subject to the annual whims of the White House and Congress.

And while both Democratic and Republican presidents have been accused of shirking the federal government’s obligations to Native Americans, college administrators, instructors and students saw Mr. Trump’s proposal as an especially dire threat that could have erased institutions that they revere as essential. Some now fear that Mr. Trump will try to squeeze the colleges throughout his presidency.

“It’s this impact on the morale of everybody,” said Ahniwake Rose, president of the American Indian Higher Education Consortium. “It’s students not knowing: ‘Do I even start school right now? What’s the point?’”

She added, “The short-term, the long-term, the ripple effects — it just continues.”

Tribal colleges, most of them in states Mr. Trump carried in last year’s election, are community anchors, often serving as fixtures of work force development efforts. They frequently have humble campuses and low public profiles, but they are sometimes the only places for dozens of miles where people have access to in-person, college-level teaching on academic subjects like chemistry and trade skills like commercial truck driving.

The colleges, while open to students who are not Native American, are also hubs of tribal life and history, curating genealogical records and tutoring people in the practical art of making moccasins. Many work to preserve vulnerable languages. Little Priest, for example, promotes itself as the only college in America that still teaches Ho-Chunk, a language of the Winnebago Tribe of Nebraska, which chartered the institution.

At N.I.C.C., chartered by the Omaha Tribe of Nebraska and the Santee Sioux Nation, classes at the campus in Macy sometimes meet in an earth lodge with walnut uprights and cottonwood rafters. This fall, the college is debuting its second baccalaureate program, a 124-credit-hour degree focusing on Indigenous environmental health. Enrollment has surged in recent years. The college had 273 degree-seeking Native students last fall, up from 109 in 2018.

Many Native students say institutions like N.I.C.C. are the only colleges where their heritages are understood and cultivated in equal measure.

“It helped me create my sense of my Native American identity,” Rosalind Grant, a student, said of N.I.C.C., where she enrolled after experiencing “culture shock” at a state university in Omaha. She struggled to connect with her peers there, she said, and her mental health suffered. She thought college was not for her.

She said that at N.I.C.C., though, “I can just openly talk — I feel more confident.”

Only weeks ago, she and other students were worried that their sanctum would not last. If the White House’s proposal had led to the gutting of N.I.C.C., Ms. Grant said, some students would have had little choice — if they wanted a college education — but “to go and live that culture shock.”

The Trump administration offered little explanation for its proposal. In addition to spending reductions for colleges, the White House recommended a cut of roughly 9 percent to the Bureau of Indian Education’s K-12 programs. It also sought to decrease the bureau’s construction budget, to $48 million from about $235 million.

But, building on hesitation among many Republicans to devastate education programs with bipartisan backing, Capitol Hill balked. The House and Senate Appropriations Committees voted last month to recommend spending the same amount of money as was spent this year, or more, on tribal education. (The House committee’s chairman, Representative Tom Cole, Republican of Oklahoma, is a citizen of the Chickasaw Nation of Oklahoma.)

In a statement, the Interior Department said the Bureau of Indian Education “remains committed to providing high-quality education that honors the unique needs and cultures of Native students.” It added that the department would “continue to advance academic excellence, student well-being and culturally relevant instruction with the resources entrusted to us.”

The department did not answer questions about the rationale for its proposal or the pushback from Congress. Tribal education advocates fear that the administration could eventually try to claw back funding through the rescission process.

To Wynema Morris, who teaches Native American studies at N.I.C.C. and has served on the college’s board and the Omaha Tribal Council, the budget proposal signaled that the Trump administration had little knowledge of the American government’s treaty responsibilities to support Native life.

“We gave up the real estate — at the point of a gun and treaties,” she said, referring to the violence and agreements that have shaped Native life for centuries. “But what did we ever get for it in return, except death, disease and destruction?”

The administration’s proposal, she suggested, could have proved to be a new act of destruction and could portend others.

Tribal colleges, she acknowledged, had faced financial pressures from other presidents. But until this year, she said, “there was never the threat of not having education.”

It is not clear what Mr. Trump might propose in the future. Earlier this year, his administration pursued dozens of layoffs at the two tribal colleges the government runs.

But a wariness has set in on campuses. Dr. Oltrogge has been building N.I.C.C.’s reserve fund and said last week that he would be “cautious and careful” moving forward.

At Little Priest, expectations are so modest that Mr. Patil said he would be delighted by even a commitment to a flat, if most likely disappointing, budget. His college and others, he noted, have little margin for error.

“Tribal colleges,” he said, “live paycheck to paycheck.”