"A large number of soldiers came about 2:30 am (0030 GMT), blowing open the locks, breaking into three buildings and banning the university guards from approaching," Ghassan Khatib, vice president of Birzeit University, told AFP.
The army seized computers, speakers and other electronic equipment used by the student council, he added.
Located in Ramallah, the university is the best-known in the West Bank, the Palestinian territory occupied by Israel since 1967.
The university published photos showing rooms ransacked, including those reserved for the student council, on its Facebook page.
Islamists affiliated to Hamas, which rules the Palestinian enclave of Gaza, won the student council elections in the university's council last April.
Al-Khatib called the raid a "violation of the university's campus and an interference in academic life," adding that it was contrary to international agreements on academic independence. The Israeli army also raided the university in June 2014.
The Israeli army confirmed the raid, saying soldiers seized "Hamas propaganda material" as it constituted an "incitement to violence".
Since October 1, Israel and the Palestinian territories have been hit by a wave of anti-Israeli stabbing, shooting and car ramming attacks.
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