Protesters, including some waving Palestinian flags, tried to block a bulldozer and scuffled with police at Khan al-Ahmar on the eastern outskirts of Al-Quds (Jerusalem). Some climbed onto the bulldozer in protest.
Israeli rights group B'Tselem said nine people were arrested -- five from the village and four others, including the organization's own head of field research.
The Palestinian Red Crescent reported 35 people injured, with four taken to hospital.
Police reported two arrests and said stones were thrown at officers.
The incident came after activists said the Israeli military had issued a warrant to the 173 residents of Khan al-Ahmar on Tuesday, authorizing itself to seize access roads to the village.
Heavy equipment was seen around the village on Wednesday, prompting speculation a road was being prepared to facilitate its evacuation and demolition.
"Today they are proceeding with infrastructure work to facilitate the demolition and forcible transfer of residents," Amit Gilutz, spokesman for B'Tselem, told AFP.
Britain's minister of state for the Middle East, Alistair Burt, visited the village in May and called on the Israeli government to show restraint.
He warned that any forced relocation "could constitute forcible transfer of people as far as the United Nations is concerned."
Such an action would be considered a violation of the Geneva Conventions.
Khan al-Ahmar is located east of Al-Quds near several major Israeli settlement blocs and close to a highway leading to the Dead Sea.
Activists are concerned continued Israeli settlement construction in the area could effectively divide the West Bank in two.
In another Bedouin village in the same region, Abu Nuwar, Israel carried out a series of demolitions Wednesday on what it described as illegally built structures.
B'Tselem said nine residential structures and three agricultural ones were demolished, leaving 62 people homeless.
The Israeli war ministry's COGAT unit for civilian affairs in the occupied Palestinian territories said the demolitions had taken place after the "owners of the buildings failed to utilize the planning procedures to their fullest extent".