The judge issued a temporary injunction allowing 60 days to respond to a petition of July 2012 in which eight villages have been cleansed.
The area is known to the IDF as Firing Zone 918. A petition against the decision was lodged by the Association for Civil Rights in Israel, on behalf of 108 Palestinian residents.
Voice of Russia, RT
Israeli police have evicted Palestinian and international activists from an area of the West Bank where Israel is planning fresh settlement building. They had put up around 20 tents in the area called E1, between Jerusalem and the Jewish settlement of Maale Adumim.
Israel's Supreme Court had ruled on Friday that the encampment could remain for six days.
Palestinians fear building in E1 would threaten the viability of a future Palestinian state.
Abir Kopty, spokeswoman for the Popular Struggle Co-ordination Committee, a Palestinian activist group, tweeted that six people had been injured during the eviction and had been taken to hospital.
Israeli police spokesman Micky Rosenfeld said there had been no injuries.
The activists had said they wanted to build a village on the site, calling it Bab al-Shams, after a famous novel about Palestinian history.
The activists' tactics in E1 had mirrored those of Israeli settlers who stake their claim to parts of the West Bank by pitching mobile homes on hilltops, known as outposts, which are not officially sanctioned, but which aim to establish "facts on the ground".
Israeli plans to develop the E1 area had been on hold for years until the Palestinians succeeded in December in having their status upgraded at the UN from an "entity" to that of a "non-member observer state".
Voice of Russia, BBC