Dr Kiyohito Yamasawa told 2,000 new students they should "quit using smartphones or quit Shinshu University" because they are "nothing more than poison to intelligence, personality and creativity".
At the 4 April welcoming ceremony in Nagano Prefecture, Dr Yamasawa said students should ditch their devices to "read books, talk with friends and make it a habit to think by yourself".
One 18-year-old who was joining the Faculty of Education said: "The president must know well about both the merits and demerits of smartphones by himself. It is inappropriate to force on students his idea that smartphones are just a bad thing."
Makoto Watanabe, a lecturer in media and communications at Hokkaido Bunkyo University, said: "I am very sympathetic to Dr Yamasawa's point of view because I see too many lazy students in classrooms when all they do is sit at the back, play games, send each other messages or surf the net.
"This has become a serious concern for teachers and university staff - although Dr Yamasawa's solution sounds quite radical."
His statement was more of a cautionary warning than a direct ruling - the university appears to have no plans to exclude students who use smartphones.
The creeping influence of technology has long been an issue in the Asian nation, where an estimated 518,000 young people are thought to be "addicted to the internet" according to the Ministry of Education.