Trump's administration has enacted massive funding cuts for academic research, curbed visas for foreign students - especially those from China - and plans to hike taxes on elite schools.
Trump alleges top U.S. universities are cradles of anti-American movements. In a dramatic escalation, his administration last week revoked Harvard's ability to enroll foreign students, a move later blocked by a federal judge.
Masaru Ishii, dean of the graduate school of medicine at Osaka University, described the impact on U.S. universities as "a loss for all of humanity."
Japan aims to ramp up its number of foreign students to 400,000 over the next decade, from around 337,000 currently.