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Foreign students and scholars traveling to Harvard were held in isolation at Boston Logan International Airport and faced visa rejections at United States consulates in the wake of President Donald Trump’s June 4 entry ban, according to a Friday court filing.

The Friday declaration was submitted by Maureen Martin, the Harvard International Office’s director of immigration services, as part of the University’s lawsuit challenging the Trump administration’s repeated attacks on its international students.

Harvard has argued that Trump’s attempt to bar entry to the U.S. on Harvard-sponsored visas — and an earlier move by the Department of Homeland Security to revoke its authorization to host international students — were abrupt and disruptive. But the moves’ full impacts are only starting to become clear.

Martin’s declaration documents, across numerous cases that were not previously reported, how international students and scholars faced distress and heightened barriers after Trump’s proclamation — in many cases, even after a judge halted the order. The people ensnared in Trump’s new rules include an Israeli professor, the CEO of an executive education program, and students and researchers from India, China, and Germany.

Trump’s proclamation immediately began to sow chaos for international students and scholars attempting to enter the U.S. when it was issued last week, Martin’s declaration shows.

Martin wrote that the HIO received reports of an unknown number of international students on at least two flights arriving at Boston Logan on June 5 who were sent to secondary inspection and detained for several hours.

The students were held incommunicado, and Martin wrote that her office “fielded inquiries from the families of international students and scholars who had no idea where their loved ones were” into the next day.

“I personally contacted [Customs and Border Protection] three or four times about the missing visa holders, but CBP was not able to confirm or deny that the visa holders were still in secondary inspection,” Martin wrote. “I also offered to send them a copy of the Court’s TRO, but they said they were waiting on guidance from ‘HQ.’”

At least two incoming J-1 visa-holders who had been in the air on June 5 or 6 were ultimately returned to their home countries of India and China.

Martin wrote that the Chinese affiliate was held for six hours in secondary inspection. Without his phone, he could not contact his family or lawyers. He was “sent back to China before he could contact HIO, and his passport was stamped to indicate that he chose to withdraw from entering,” Martin wrote.

A federal judge temporarily blocked Trump’s proclamation the evening of June 5, and the block is still in effect. But at least three Harvard affiliates, including the researcher who was returned to India, were still turned away on the basis of the proclamation.

The Crimson reported last week that one Harvard affiliate — a postdoctoral researcher seeking a J-1 visa at the U.S. consulate in Munich — was denied a visa after the judge’s temporary restraining order had gone into effect. Martin’s declaration shows that he was one of at least two affiliates who were turned away in Munich.

A second visa applicant in Munich, who was seeking an F-1 visa to attend Harvard Business School, was also denied a visa on June 6.

Both of the applicants in Munich were told their visas were denied because of Trump’s proclamation, even though it had already been halted. Both applicants objected, and a consular officer told one that they were “just following orders” in rejecting the visa.

The other applicant said he was told by a consular officer that “I receive my orders from Washington.”

The Trump administration has aggressively stepped up its screening of Harvard affiliates’ social media accounts, and it ordered a pause on scheduling visa interviews in late May. Since then, some affiliates have struggled to put appointments on their calendar.

On June 8, the U.S. consulate in Tel Aviv canceled a June 11 visa appointment for a visiting professor from Israel, three days after the TRO blocking the executive order had gone into effect. The visiting professor was scheduled to travel to the U.S. on July 13 to teach a summer school course at Harvard beginning on July 14 — but is still unable to book an interview appointment for a J-1 visa, according to the filing.

The uncertainty has also made Harvard’s external partners anxious.

Martin wrote in the filing that an international executive education program ended a partnership with Harvard Medical School because of concerns over Harvard’s ability to back international student visas.

The CEO of the program canceled the partnership after he was refused a visa by a U.S. consulate because of the program’s ties to HMS and he grew worried about student safety, according to Martin.

One third-party sponsor withdrew a $50,000 grant it had offered to an incoming Harvard Law School student in the Master of Laws program due to the challenges facing Harvard’s international students. The sponsor told the student they were willing to help the student find placement at another university.

Citing an expedited admissions program for current Harvard students rolled out by a Turkish university, Martin wrote that other universities around the world have capitalized on the uncertainty regarding Harvard’s ability to host international students to recruit away talent.

“At this time, Harvard cannot assure its international students and scholars that they will be able to travel to Cambridge to study at Harvard free from disruption caused by the federal government, which could occur without notice and have immediate effect,” she wrote.

The federal judge overseeing Harvard’s lawsuit has indicated that she will grant a preliminary injunction in the case, extending the halt on the DHS order until she reaches a decision.

Harvard and the federal government submitted competing versions of proposed injunctions Thursday, which encompasses both the White House’s May 22 revocation of Harvard’s Student and Exchange Visitor Program certification and Trump’s proclamation.

The two sides clashed over whether Harvard should be granted an additional 30 days before its SEVP certification could be withdrawn, and whether there should be a clause in the injunction preventing the White House from imposing a “categorical restriction” on Harvard’s ability to host non-immigrant F or J visas.

—Staff writer Samuel A. Church can be reached at samuel.church@thecrimson.com. Follow him on X @samuelachurch.

—Staff writer Cam N. Srivastava can be reached at cam.srivastava@thecrimson.com. Follow him on X @camsrivastava.