The graffiti, sprayed on the outside of the mosque and accompanied by the star of David, reads "slated for demolition" and "there will be a war for Judaea and Samaria" the biblical name of the occupied West Bank.
The police were not immediately available for comment.
The incident comes as leaders of Israel's 1.3 million-strong Palestinian minority have come under attack for their support of a Gaza aid flotilla seized by the Israeli navy in international waters after a deadly confrontation in which naval commandos shot dead nine Turkish activists.
Haneen Zuabi, an Arab member of the Israeli parliament, received death threats and was accused of being a traitor by fellow lawmakers after taking part in the six-ship flotilla that aimed to break Israel's blockade of Gaza.
Ahmed Tibi, another Arab MP who did not take part in the flotilla, has also received death threats.
The Al-Aqsa Foundation linked the desecration of the mosque to the "atmosphere of hatred and racism against Arabs and Muslims in this country on the official and popular level."
The foundation is linked to the radical wing of the Islamic Movement led by Sheikh Raed Salah, who was also on one of the ships.
Israel's Arab citizens, who make up nearly 20 percent of the population, are the descendents of Palestinians who remained in the Jewish state following the 1948 war that attended its creation.
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