According to local media, several hundred settlers who had barricaded themselves inside makeshift structures threw stones at police officers and tried to prevent the evacuation.
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During the evacuation, eight protesters were injured and five arrested, i24NEWS reports, citing police.
All victims received medical care, some of them were taken toHadassah Ar a-Tsofim hospital in Jerusalem.
An operation to dismantle Amona, authorised by Israel's High Court of Justice, started on Wednesday. The court said the settlement was built on privately-owned Palestinian land.
The new settlement that Israel is planning will be the first government-authorised West Bank settlement to be built in about 25 years.