WASHINGTON — Since Hurricane Maria’s deadly rampage last September, the Education Department has doled out tens of millions of taxpayer dollars in disaster relief to colleges and universities supposedly affected by last year’s hurricanes.

Only a fraction has gone to institutions where the storm had its most profound impact: Puerto Rico.

Instead, elite institutions like New York University and the University of Southern California have received aid, as have Liberty University, the Christian school in Virginia run by President Trump’s ally Jerry Falwell Jr., and Grand Canyon University, a Christian, for-profit college in Arizona. Some of those universities have been clear about why they took the money — N.Y.U. had already enrolled Puerto Rican students temporarily displaced by the storm when the Education Department forwarded funds to defray the costs. Others, like Grand Canyon, have refused to explain with any detail.

And while Puerto Rico’s share of the aid was roughly in line with states also affected by last year’s hurricanes, like Florida, the devastation is not at all comparable.

“Here, no one was spared,” said Carmen J. Cividanes-Lago, executive director of the Association of Private Colleges and Universities of Puerto Rico (ACUP), a nonprofit member group of private higher education institutions that serve more than 114,000 students in Puerto Rico.