The Trump administration has intensified its conflict with Harvard University, with federal agencies notifying the New England Commission of Higher Education that the Ivy League school might no longer fulfill accreditation standards due to breaches of federal antidiscrimination regulations.

The Department of Education and Department of Health and Human Services issued a letter to NECHE on Wednesday, indicating that it must collaborate with Harvard to address these violations or revoke the 388-year-old institution’s accreditation.

“Harvard has been — and is — deliberately indifferent to the severe, pervasive, and objectively offensive harassment of Jewish and Israeli students by its own students and faculty,” stated Paula M. Stannard, Director of the HHS Office of Civil Rights, in the letter.

“By allowing antisemitic harassment and discrimination to persist unchecked on its campus, Harvard University has failed in its obligation to students, educators, and American taxpayers,” said Secretary of Education Linda McMahon.

In addition to signaling that an institution of higher learning meets certain quality and integrity standards, accreditation “is required for institutions to receive federal financial aid, including student loans and grants,” according to NECHE.

“When an institution — no matter how prestigious — abandons its mission and fails to protect its students, it forfeits the legitimacy that accreditation is designed to uphold,” HHS Secretary Robert F. Kennedy Jr. said.

The missive follows a shot across the bow fired last month by Trump’s Joint Task Force to Combat Anti-Semitism, which warned Harvard president Alan Garber that the university was in violation of federal civil rights laws over campus antisemitism and that its federal funding was at risk.

“Failure to institute adequate changes immediately will result in the loss of all federal financial resources and continue to affect Harvard’s relationship with the federal government,” the June 30 letter said.

The letter was accompanied by a 57-page report by HHS detailing its findings resulting from 50 “listening sessions” held with Jewish Harvard students, which the agency alleges constitutes a “pattern of unlawful and unchecked discrimination” at the university.

After the letter was sent, the Commission put out a fact sheet explaining how the accreditation process works, noting that the federal government cannot actually force it to withdraw a university’s accreditation.

“The Commission’s policies and procedures, in accord with federal regulation, give institutions up to four years to come into compliance when found by the Commission to be out of compliance, which can be extended for good cause. Institutions in a non-compliance status remain accredited during this period of time,” The Hill reported.

In a statement to The Post, a Harvard spokesman said the university has “taken substantive, proactive steps to address the root causes of antisemitism in its community,” highlighting the sharing of its recent Antisemitism and Anti-Israel Bias Report, as well as “strengthened policies, disciplined those who violate them, encouraged civil discourse, and promoted open, respectful dialogue,” the statement read.

“Harvard has made significant strides to combat bigotry, hate and bias. We are not alone in confronting this challenge and recognize that this work is ongoing. “

Last month, the DOE sent a similar letter to the Middle States Commission on Higher Education, an accrediting institution that Columbia University belongs to, saying it, too, should lose its accreditation over its failure to contain antisemitism on its campus in Manhattan’s Morningside Heights neighborhood.

The Trump administration also slapped Harvard with a subpoena Wednesday as part of its probe into the school’s foreign student exchange program — with Department of Homeland Security Secretary Kristi Noem claiming the institution has “allowed foreign students to abuse their visa privileges and advocate for violence and terrorism on campus.”

Trump had said he wants to curtail its admission of international students, which the Wall Street Journal estimates could cost the school $90 million a year in lost tuition.

A federal judge issued a temporary injunction on the ban last month, which the administration has vowed to appeal.

The administration has also yanked some $3.2 billion in federal contracts and grants from Harvard, and pulled around $700 million in federal research funds.