The elite universities are asked to disclose details of gifts from Saudi Arabia and China.
The US has launched investigations into Harvard and Yale universities over suspicions they received undisclosed funds from foreign countries, including Saudi Arabia and China.
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.
What are Harvard and Yale accused of?
The Department of Education said Yale University had chosen not to report any foreign funding over the last four years, and is suspected of failing to disclose at least $375m in foreign gifts and contracts.
The agency said it was also concerned that Harvard lacked "appropriate institutional controls over foreign money" and had failed to fully report foreign gifts and contracts.
Earlier this month, the chairman of Harvard's chemistry department and two Chinese researchers were charged with making false statements about ties to the Chinese government.
In letters to the Ivy League universities, the Department of Education called on them to supply the names and addresses of foreign sources involved in contracts and gifts, as well as the activities supported by the funding since August 2013.
Harvard was asked to disclose records involving the governments of China, Qatar, Russia, Saudi Arabia and Iran, as well as companies including Chinese technology giant Huawei.
Officials called on Yale to disclose similar information about foreign contributions.
Yale did not comment on the allegation that it had failed to report $375m in foreign gifts and contracts, but told the BBC it was preparing a response to the government's letter. Harvard said it was also preparing a response. BBC