“Foreign government spending on U.S. schools is effectively a black hole,” the report concluded.

The same month, Education Department officials revealed in congressional testimony that fewer than 3 percent of 3,700 higher education institutions that receive foreign funding reported receiving foreign gifts or contracts exceeding $250,000.

The investigations are the latest example of how colleges and universities have found themselves in the cross fire of the Trump administration’s aggressive immigration and American foreign policy. International enrollment has declined, visa delays have increased, and foreign students and staff members have been denied entry. This week, a Palestinian student headed to class at Harvard said he was denied entry into the country after a Customs and Border Protection agent demanded to see his phone and objected to the social media activity of his friends. Amid pressure from lawmakers and an escalating trade war with China, a number of colleges — including Texas A&M — have shuttered their Confucius Institutes.

But the most recent charge by the Education Department has rattled those in higher education. The investigations, disclosed in the Federal Register, were the first time in recent history that the department had publicly announced that it was scrutinizing specific schools. Those notices detailed extensive information — including tax records and wire transfers, communications between professors and foreign governments, and information about overseas campuses — that the department wanted.

The department is also seeking comprehensive records on China and Qatar. The department’s notices repeatedly cite high-profile organizations, such as the Qatar Foundation for Education, Science and Community Development, which helps fund American satellite campuses in the country; the Office of Chinese Language Council International, also known as “Hanban,” which runs Confucius Institutes; and Huawei, the largest telecommunications equipment producer in the world, which the Trump administration deems a national security risk, and which Secretary of State Mike Pompeo called “an instrument of the Chinese government.”

The Education Department investigations have caused friction between the department and several higher education groups, which have urged it to clarify the rules around an obscure provision, called Section 117, in the Higher Education Act. They say that university relationships with foreign entities have become more complex and voluminous since the section was added three decades ago. In the absence of any formal regulation from the department, schools have reported based on their best interpretations of the law, the groups say.

“This is what happens when you pass a law that nobody looks at ever again,” said Terry W. Hartle, senior vice president of the American Council on Education, which represents 1,700 college and university presidents and higher education executives.