Some stones were thrown by the settlers and barricades of tyres were set on fire as the authorities enforced an order that they be moved on ahead of the settlement being demolished.
Some protesters were detained after scuffles broke out.
There are more than 250 Jewish settlers living on the Amona settlement, which is on privately owned Palestinian land seized during the 1967 six-day war.
The legal battle over Amona has dragged on for eight years, with the latest ruling ordering that it be evacuated by 8 February.
Columns of Israeli police are at the settlement.
The settlers have said they will not resist violently, but they will make it as difficult as possible for the authorities to evict them.
One of the settlers’ leaders, Avihai Bavaron, said: “We won’t leave our homes on our own. Pull us out, and we’ll go.
“It is a black day for Zionism.”
Sky News Middle East Correspondent Alex Rossi is at Amona.
“This is one of about 100 illegal outposts. Amona has been deemed for demolition by the Supreme Court,” he said.
“Now the people who live here have been joined by people from the settlers’ movement and they are resisting that evacuation.”
There was a violent partial eviction in Amona in 2006, when nine homes were torn down by the authorities.
Police were confronted by thousands of settlers and more than 200 people were injured.
Hours before the latest police operation, Israel announced plans for 3,000 more settlement homes in the West Bank.
It is the third such declaration in 11 days since President Donald Trump took office.
Mr Trump has signalled that he may be more sympathetic toward such projects than his predecessor Barack Obama.
Palestinians and the EU criticised an Israeli announcement a week ago that it would build about 2,500 more homes in the West Bank.
It followed approval days before of more than 560 new homes in East Jerusalem.