Harvard has so far defied Trump’s calls to submit to oversight of its curriculum, staffing, student recruitment, and “viewpoint diversity”.
Trump has cut federal grants for Harvard and tried a host of different tactics to block the institution from hosting international students.
The administration has sought to remove Harvard from an electronic student immigration registry and instructed embassies to deny visas to international students hoping to attend the Massachusetts-based university.
The administration insists its moves are legally justified over Harvard’s failure to protect Jewish students, particularly amid campus protests against Israel’s war in Gaza.
Harvard has sued the Department of Homeland Security and other agencies to block the efforts, arguing they are illegal and unconstitutional.
The Ivy League institution has also sued to restore more than US$2 billion ($3.3b) in frozen funds.
A Harvard spokesman did not immediately respond to a request from AFP for its response to the State Department investigation.
- Agence France-Presse