The Trump administration’s efforts to halt Harvard University’s ability to enroll international students has sown “profound fear, concern, and confusion”, the university’s director of immigration services said in a court filing on Wednesday.

Countless international students have asked about transferring, the director, Maureen Martin, wrote in the filing.

Many others are afraid to go to their own graduations, she said.

A handful of American students have also expressed hesitation about attending a school without international students. And several students claimed to have been hassled at airports because of their Harvard visas, the court filing said.

It was a part of a Harvard lawsuit against the Trump administration in response to its efforts to ban international students at the school. A judge moved last week to temporarily block the government’s move, and the two sides will face off in court on Thursday for the first time.

“Many international students and scholars are reporting significant emotional distress that is affecting their mental health and making it difficult to focus on their studies,” Martin wrote.

The Trump administration’s directive, if it were allowed to go into effect, would affect 5,000 Harvard students, along with 2,000 recent graduates participating in a work programme called “optional practical training”. The order also affects incoming students.

It is the latest attack on Harvard from the Trump administration, which has singled out the 388-year-old university, accusing it of failing to crack down on antisemitism. The administration has also frozen about $3 billion in grants and contracts to the university’s researchers.

The Trump administration also asked for extensive information about Harvard’s international students before the department of homeland security, which oversees the entries of international students, announced a ban on their enrollment at the school.

In that announcement, the department accused Harvard’s leaders of creating “an unsafe campus environment by permitting anti-US, pro-terrorist agitators to harass individuals, including many Jewish students, and otherwise obstruct its once-venerable learning environment”.