Israel moved three bulldozers to the village, Khan al-Ahmar, earlier in the day though demolition had yet to begin, after the military left a land confiscation notice there on Tuesday.
Around 180 Bedouin, raising sheep and goats, live in tin and wood shacks in Khan al-Ahmar. It is situated between Maale Adumim near Jerusalem, and a smaller settlement to the northeast, Kfar Adumim.
Khan al-Ahmar was built without Israeli permits, which Palestinians say are impossible to obtain. Israel has long sought to clear Bedouin from the area between the two settlements, and the Supreme Court approved the demolition in May.
Removing the Bedouin, human rights groups say, would create a bigger settlement pocket near Jerusalem and make it more difficult for Palestinians to achieve territorial contiguity in the West Bank, a territory they say they seek along with the Gaza Strip for a future state.
Israel says it poses a threat to security due to its proximity to a highway.
At Khan al-Ahmar, several dozen Palestinians scuffled with Israeli police. A Palestinian ambulance service said 35 protesters were hurt and four of them were taken to hospital. Police said two people were arrested.
Police spokesman Micky Rosenfeld said 11 people were arrested in the "disturbance" including several for throwing stones at officers in Khan al-Ahmar. He said three officers were injured, including one evacuated to a hospital for treatment.
"I was born here and will not move anywhere else," said Feisal Abu Dahok, 45. "If they destroy the village, we will build it again here or nearby."
Israel said it plans to relocate the residents to an area about 12 kilometres (seven miles) away, near the Palestinian village of Abu Dis.
The new site is adjacent to a landfill and rights advocates say that a forcible transfer of the residents would violate international law applying to what they describe as "occupied" territory.
Palestinians argue that the West Bank, which Israel captured from Jordan in the 1967 Six-Day War, is occupied territory, while Israel argues that it is disputed land.
At a news briefing in Geneva on Tuesday, a spokeswoman for the UN human rights office expressed concern at reports of impending demolition.
"For more than a decade people in the Khan al-Ahmar community ... have resisted efforts to move them to make way for settlement expansion," the spokeswoman, Liz Throssell, said.
She said "international humanitarian law prohibits the destruction or confiscation of private property by the occupying power", a reference to Israel.
Khan al-Ahmar's residents belong to the Jahalin tribe of Bedouin who were expelled from southern Israel by the military in the 1950s.
The UN's main human rights body on Tuesday called on Israel to abandon the demolition plans.
Associated Press contributed to this report.