Protesters, including some waving Palestinian flags, tried to block a bulldozer and scuffled with police at Khan al-Ahmar, east of Jerusalem. Some climbed onto the bulldozer in protest.
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Israeli police said 11 people were arrested. Israeli rights group B'Tselem said they included the organisation's own head of field research.
The Palestinian Red Crescent reported 35 people injured, with four taken to hospital. Police said the wounded included three officers, including one taken to hospital.
Police 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, authorising soldiers 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.
Israeli authorities say the village and its school were built illegally, and in May the supreme court rejected a final appeal against its demolition.
But activists say the villagers had little alternative but to build without Israeli construction permits, as the documents are almost never issued to Palestinians for building in parts of the West Bank where Israel has full control over civilian affairs.
Israel authorities say they have offered villagers an alternative site.
The village is made up mainly of makeshift structures of tin and wood, as is traditionally the case with Bedouin villages.
It is unclear when the demolition will take place.
'Deeper hole'
Senior Palestinian official Saeb Erekat condemned the demolition plans and appealed to the international community.
"Are we coming to see one day that Israel can be held accountable?" he asked journalists in Ramallah.
"If not, it means you're pushing this region towards a deeper hole of violence and counter-violence and extremes."
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."
Forcible transfer is considered a violation of the Geneva Conventions.
Khan al-Ahmar is located east of Jerusalem 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 defence 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 utilise the planning procedures to their fullest extent".
"This despite the fact that they were given the opportunity to enquire in the matter and were told that if they did not, the illegal construction would be demolished," it said in a statement.
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