The Cosmic Watchdog

The Trump administration directive seeking to pause federal financial assistance seeded widespread chaos and concern across the educational landscape on Tuesday, from early childhood programs to university research efforts.

At least one university leader urged professors to pause spending on research projects. The cash flow for Head Start, the early childhood education program that serves 800,000 children, was cut off in some places before the federal government clarified that the program was not included in the directive.

And there was widespread uncertainty over which other programs might face scrutiny or be dismantled.

The directive would pause funding at least until mid-February while the government investigates whether programs align with President Trump’s policy priorities, including ending “D.E.I., woke gender ideology and the Green New Deal.” By Tuesday afternoon, a federal judge in Washington, D.C., had blocked it in response to a lawsuit.

But the day unfolded in a kind of whiplash, as educators and students frantic about federal programs scrambled to understand how the directive might affect them. The Trump administration clarified that some programs, like Pell grants and funding for low-income schools and disabled children, would be exempt and sought to push back on early fears of funding being cut for children.

Some Head Start providers were blocked when attempting to access a federal online payment portal on Tuesday, setting off a panic for program directors who worried that they would not be able to make payroll in the next pay period. A few moved to lay off staff because of the uncertainty, before a clarification was issued by the administration.

Katherine Baicker, provost of the University of Chicago, asked university researchers not to make additional spending commitments, purchase new supplies or equipment, start new experiments or embark on funded travel.

“This is not a request that I make lightly,” she said in an email obtained by The New York Times. “The research enterprise is at the core of our university’s mission and is of profound importance to the daily work of our faculty, researchers, staff and students.”

She said in the email that the university was struggling to understand the full effect of the directive and she wished she had more information. “But we must for now proceed under the assumption that grant expenditures incurred after today while this memorandum is in effect may not be covered by federal funding,” she wrote.

Daniel W. Jones, a former chancellor of the University of Mississippi who also led the medical school there, said universities would have to decide whether to tap their own money to sustain projects if the pause resumed. Wealthier flagship institutions would have the funds to continue their research, but would have to worry about the legal risk of defying the directive, he said.

But more financially precarious institutions may find their research in jeopardy.

The Association of Public and Land-Grant Universities put out a statement calling the pause “overly broad” and “unnecessary and damaging.”

“While we understand the Trump administration wants to review programs to ensure consistency with its priorities, it is imperative that the reviews not interfere with American innovation and competitiveness,” the association’s president, Mark Becker, said. He called for the Trump administration to rescind the directive.

The association said the directive could disrupt researchers working on projects ranging from cures for cancer to supporting American farmers.

Ted Mitchell, president of the American Council on Education, which represents colleges and universities, said in an interview that the organization’s priority was “to make sure that Pell grant funds will continue to flow,” referring to financial aid for low-income students. “We’re not going to exclude students from our campuses,” he said. “That’s not what we do.”

But later in the day, a spokeswoman for the Department of Education, Madi Biedermann, said that the pause did not apply to Pell grants. The Department of Education clarified that the directive only applied to discretionary grants, and not to formula grants, like Title 1, which provides aid to high-poverty schools, or the Individuals with Disabilities Education Act, which supports children with disabilities.

Some 3,000 people joined a hastily convened webinar by the American Council on Education on Tuesday afternoon to try to decode the directive.

In a statement, AASA, the school superintendents association, said the fate of other federal funding streams used to pay for school meals, aid to Native American students and specific educational programs was uncertain.

“Yesterday’s announcement includes a lot of information without a lot of specifics,” AASA said. “Given the very unique approach of the proposal, we can’t, with the information the president has released, have any certainty on what it will mean.”

Other education officials said they were trying not to overreact. Public school leaders in Clark County, Nev., which includes Las Vegas, told employees in a letter that they “do not anticipate an immediate interruption to district programs and students’ services.”

Most researchers “are willing to take a deep breath,” said Karl Scholz, president of the University of Oregon. And Jim Henderson, the president of Louisiana Tech University, said school officials did not believe the directive, which was issued Monday night, was so sweeping as to cut off support for existing projects there.

“I couldn’t be less in freakout mode on this communication,” he said. “It doesn’t appear to be targeted toward anything we pursue at this university.”

But Dr. Henderson said that if future orders threatened work at Louisiana Tech, school officials would appeal to the state’s congressional delegation for help.

Some researchers were scratching their heads over how a directive seemingly concerned with “woke” education might be applied to them. Universities were not sure how far, exactly, the directive reached.

“There is certainly concern and fear, but we are still trying to wrap out arms around the scope of the impact,” said Charles L. Welch, the president of the American Association of State Colleges and Universities, which includes many regional schools and historically Black institutions.

Bruce Fuller, an education researcher at the University of California, Berkeley, predicted that a pause could backfire.

“Research on top administration priorities, like parent vouchers or charter schools, will go undone if the department insists on censoring scientific findings,” he said.

Dr. Fuller is conducting research to determine how Covid-19 pandemic recovery funding has affected the performance of California students. On Tuesday, he said, the Department of Education informed researchers on the project that they must not post any new material about their research on the web, or on social media, without written approval from Ms. Biedermann.

At least one university researcher said her project had already been shut down under a different order issued last week. Meredith Dank, a professor at the N.Y.U. Marron Institute of Urban Management, had grants from the U.S. State Department for five projects — in Thailand, India, Tanzania, Kenya and Costa Rica — meant to combat human trafficking.

On Friday evening, she got an email from the State Department stating that all foreign aid was being paused for 90 days while the agency reviewed how each program aligned with national priorities and agenda. That put all of those grants on hold.

Then, on Saturday evening, she heard that the grant in Thailand had been terminated.

That grant was the only one specifically “focused on L.G.B.T.Q. individuals who were at risk or had been sex trafficked,” she said. For the $4 million, five-year program to be terminated was “heartbreaking,” Dr. Dank said. The local staff members involved still “can’t believe that it’s true.”