Ayman Odeh said made the remarks following Al Aqsa Mosque's closure after Friday's attack by three Israeli-Arab gunmen.
The leader of the Arab bloc in the Knesset said: "Closing the Al Aqsa Mosque is explosive. The second Intifada broke out on al Aqsa. I warn against the third," according to the Jerusalem Post.
He criticized the attack, saying that Israeli Arabs should wage a "political struggle, and not in any way an armed struggle."
MKs from the Islamic Movement-affiliated United Arab List party and the Ta'al party, both part of the Joint List, also released statements condemning violence.
Odeh added that Prime Minister Benjamin Netanyahu "wants to turn the conflict from a political to a religious one, which is why he backs provocative entry by settlers into the area of the mosque."
Jews are not allowed in the close vicinity of the mosque, but they are allowed in the Temple Mount Plaza, where they are prohibited from praying.