Interior Ministry spokeswoman Sabine Haddad said Chomsky was turned away for "various reasons" but declined to elaborate. Chomsky was trying to cross the Allenby Bridge from Jordan. He was scheduled to deliver a lecture at Bir Zeit University in the West Bank.
Haddad said her ministry was looking into allowing him to enter only the West Bank.
Chomsky told Channel 10 TV from Jordan Sunday: "I've often spoken at Israeli universities."
Chomsky is one of Israel's harshest academic critics. After Israel's 2009 war in Gaza, he was quoted as saying, "supporters of Israel are in reality supporters of its moral degeneration."