ReutersHarvard University filed a federal lawsuit against the Trump administration to stop billions of dollars in proposed cuts.
The suit filed Monday is part of a feud that escalated last week when the elite institution rejected a list of demands that the Trump administration said was designed to curb diversity initiatives and fight anti-semitism at the school.
President Donald Trump froze $2.2bn (£1.7bn) of federal funding and also threatened the university's tax-exempt status.
"The consequences of the government's overreach will be severe and long-lasting," Harvard's president Alan M. Garber said in a letter to the university on Monday.
The White House responded later Monday night in a statement.
"The gravy train of federal assistance to institutions like Harvard, which enrich their grossly overpaid bureaucrats with tax dollars from struggling American families is coming to an end. Taxpayer funds are a privilege, and Harvard fails to meet the basic conditions required to access that privilege", said White House spokesman Harrison Fields.
Mr Garber said the funding freeze affected critical research including studies on pediatric cancer, Alzheimer's disease and Parkinson's disease.
"In recent weeks, the federal Government has launched a broad attack on the critical funding partnerships that make this invaluable research possible," the school's lawsuit said.
"This case involves the Government's efforts to use the withholding of federal funding as leverage to gain control of academic decisionmaking at Harvard."
Aside from funding, the Trump administration days ago also threatened Harvard's ability to enroll international students.
Mr Garber, who is Jewish, acknowledged Harvard's campus has had issues with anti-semitism but said he had established task forces to work with the problem. He said the university would release the report of two task forces that looked into anti-semitism and anti-Muslim bias.
The prominent US university, located in Massachusetts, is not the only institution faced with withholding of federal dollars, which play an outsized role in funding new scientific breakthroughs.
The administration has targeted other private Ivy League institutions including suspending $1bn at Cornell University and $510 million at Brown University.
Others such as Columbia University, the epicentre of pro-Palestinian campus protests last year, have agreed to some demands after $400 million of federal funds was threatened.
The demands to Harvard included agreeing to government-approved external audits of the university's curriculum as well as hiring and admission data. In response, Harvard released a blistering letter rejecting them.
"The university will not surrender its independence or relinquish its constitutional rights," Harvard's lawyers told the administration on April 14.
"Neither Harvard nor any other private university can allow itself to be taken over by the federal government. Accordingly, Harvard will not accept the government's terms as an agreement in principle."
Former US President Barack Obama, a Harvard alum, said he supported the university.
