The Trump administration renewed its assault on Harvard University on Friday, filing a lawsuit in Massachusetts alleging the Ivy League institution violated the civil rights of Jewish and Israeli people in the aftermath of the war in Gaza.

The lawsuit, shared publicly by the New York Times, accuses Harvard of allowing anti-Israel protesters to operate on campus “with impunity” following the 2023 Hamas terrorist attack on Gaza and Israel’s massive military response.

Donald Trump said last month he wanted a $1bn payout from Harvard for its perceived antisemitism, and Friday’s development is the latest in a series of legal attacks on one of the nation’s most prestigious universities since he returned to the presidency last year.

In September, a federal court ruled the Trump administration unlawfully canceled $2.2bn in federal research grants as part of the president’s feud, punishing Harvard for defying his directives to end diversity, equity and inclusion programs and “leftwing” ideological teaching even as other institutions fell in line and made huge financial settlements.

The lawsuit, filed Friday in the US federal court for the district of Massachusetts, the Times reported, reignited a feud that the September ruling appeared to have settled.

Harvard, the 44-page court filing said, “turned a blind eye to antisemitism and discrimination against Jews and Israelis” by strictly enforcing policies against other forms of bias but allowing anti-Israel protests, such as a three-week “encampent” by pro-Palestinian demonstrators in 2024, to proceed virtually unchecked.

Jewish and Israeli students, it said, “were repeatedly denied access to educational facilities by antisemitic demonstrators” as well as “harassed, physically assaulted, stalked, and spat upon.

“Fearful for their safety, Jewish students wore baseball caps to conceal their yarmulkes, or kept out of sight,” it said, claiming that Harvard’s response was to “do nothing”.

“Harvard fostered and continues to foster a campus climate where hostile antisemitism and anti-Israeli conduct thrives,” the lawsuit alleges.

Trump has previously accused Harvard of being “strongly antisemitic” and that it had done “a terrible job” in dealing with the protests.

In a statement last April, Alan Garber, Harvard’s president, rejected the president’s allegations but conceded the university had work to do.

“Harvard takes that work seriously. We will continue to fight hate with the urgency it demands as we fully comply with our obligations under the law. That is not only our legal responsibility. It is our moral imperative,” he said.

Harvard also countersued the administration, accusing it of trying to “gain control of academic decision-making”. Garber insisted “the university will not surrender its independence or relinquish its constitutional rights”.

In its latest filing, the government is asking the court to rule Harvard in breach of Title VI – which prohibits discrimination on the basis of race, color, or national origin in any program or activity receiving federal financial assistance.

If successful, it could block the distribution of up to $9bn in future grants, and allow it to try to recoup money previously awarded. Time reported last May that federal money for research funding made up 11% of the university’s operating revenue in 2024, and other estimates say Harvard receives up to $800m each year directly from the government.

University leaders have warned that without federal money, multiple crucial science and medical research programs, including in the areas of cancer and heart disease, would “come to a halt midstream”.

The Friday lawsuit against Harvard is the second time in a month the Trump administration has sued Harvard. A justice department filing last month said the university had failed to comply with a requirement to provide data showing affirmative action was no longer part of student admission protocols.

An executive order by the president last year banning Harvard’s foreign student population from entering the US was blocked by a federal judge in Boston.

The Guardian has contacted Harvard for comment.