The US Department of Education said the elite schools did not fully report hundreds of millions of dollars in foreign gifts and contracts.
Harvard and Yale told the BBC they were preparing responses for the government.
It comes amid a clamp down on foreign funding to academic institutions.
Under US law, universities are required to report all gifts and contracts from foreign sources that exceed $250,000 (£193,000).
Since July, the Department of Education said it had uncovered some $6.6bn in previously unreported gifts from countries including Qatar, China, Saudi Arabia and the United Arab Emirates. It said this figure could be "significantly underestimated".
Officials have previously described foreign spending on US universities as a "black hole" and warned that such money can come with strings attached.
"This is about transparency. If colleges and universities are accepting foreign money and gifts, their students, donors, and taxpayers deserve to know how much and from whom," said US Secretary of Education Betsy DeVos.
"Unfortunately, the more we dig, the more we find that too many are underreporting or not reporting at all," she said.