The authorities said the three buildings had been built without licenses in "Area C" of the Israeli-occupied West Bank, Palestinian activist Rateb al-Jabour told The Anadolu Agency.
He said the school had been set up early this year through a grant from a European institution.
Al-Jabour added that around two dozen Palestinian students currently attended classes at the school.
The Israeli authorities did not say when the three buildings would be demolished.
Israel prohibits Palestinians from building homes – or other structures – in locations designated as part of "Area C" under the Washington-sponsored Oslo Accords.
Signed in 1995 between Israel and the Palestinian Authority, the accords divide the West Bank into three parts, including "Area C," which – accounting for around 60 percent of the Palestinian territory – remains under Israeli security and administrative control.