Village councillors and Palestinian security officials blamed Israelis from a nearby settlement for the attack.
The area is home to some of the most hardline settlers who advocate a "price tag" policy under which they target Palestinians in retaliation for any Israeli government measure they see as threatening Jewish settlements.
The Israeli military said "it appears that the suspects wrote hate-filled messages in Hebrew in addition to burning bookshelves and a carpet."
It assured the Palestinian Authority that it "views the incident gravely" and that security forces are working to locate the perpetrators, the statement said.
Last week, a house and three vehicles were set on fire in another village, also near the West Bank city of Nablus. The owner of the house told police he saw three Jewish settlers start the fires.
Settlers have expressed outrage over the government's decision to impose a 10-month moratorium on new building permits for Israeli homes in the occupied West Bank, outside annexed Arab east Jerusalem.
Many settlers consider they have a God-given right to live in the biblical Land of Israel, which includes the West Bank.