M.I.T. became the first university to reject an agreement that would trade support for the Trump administration’s higher education agenda in exchange for favorable treatment.

The proposal, called the “Compact for Academic Excellence in Higher Education,” was sent to nine universities and would require colleges to cap international student enrollment, freeze tuition for five years, adhere to definitions of gender and prohibit anything that would “belittle” conservative ideas.

In a letter on Friday to the Trump administration, M.I.T.’s president, Sally Kornbluth, wrote that the university has already freely met or exceeded many of the standards outlined in the proposal, but that she disagrees with other requirements it demands, including those that would restrict free expression.

“Fundamentally, the premise of the document is inconsistent with our core belief that scientific funding should be based on scientific merit alone,” Dr. Kornbluth wrote.

The White House, which did not immediately respond to a request for comment, has said it wants responses from the universities by Oct. 20. The other eight colleges are the University of Arizona, Brown University, Dartmouth College, the University of Pennsylvania, the University of Southern California, the University of Texas, Vanderbilt University and the University of Virginia.

The compacts have been deeply unpopular among faculty members, who view them as yet another political intrusion into the affairs of academia. They argue that the Trump administration is threatening the independence of American higher education by cutting hundreds of millions of dollars in research funding to force top universities to adopt its agenda.

This is a developing story. Check back for updates.