Multiple "price tag" attacks have been carried out in recent months since the IDF declared the Kumi Ori outpost near Yitzhar a closed military zone.
Dozens of tires were slashed and graffiti were uncovered in the village of Jish.
The graffiti on the wall of the mosque read, "[They're] destroying the Jews? Kumi Ori will destroy the enemy!"
Police have opened an investigation into the incident and are gathering evidence and searching for suspects.
The rabbis dubbed the phenomenon a "slippery slope," while the education staff condemned the attacks.
MK Touma-Sliman: If price tag attackers are ignored, there will be a pogrom on the Palestinians
Price tag attacks were reported in the Palestinian villages of Deir 'Ammar and as-Sawiya and the Arab-Israeli city of Tayibe in which cars were vandalized and an olive tree grove was uprooted.
Jewish residents say IDF protects Palestinians, human rights organizations note uptick in violence against Arabs by settlers.
It was one of a number of instances of graffiti in a hate crime attack allegedly carried out by extremist right-wing Jewish Israelis in the predawn hours of Sunday.
The tires of 21 cars were slashed and pro-settler graffiti was sprayed in an Israeli-Arab town in northern Israel, the second such incident this week.