The homes in the Ofra settlement -- a symbol of Jewish settler defiance to international concerns -- were found to have been built on private Palestinian land and ordered razed by March 5.
Police cleared protesters from the houses one at a time over several hours, an AFP reporter said.
They had cleared eight of the nine houses but dozens of predominantly young protesters made a final stand on the roof of the ninth.
While still trying to clear the final home, bulldozers demolished one house, the reporter said.
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Leaders of the Ofra community said they were intent on preventing major clashes like those during the eviction of the nearby Amona settlement three weeks ago, where youths barricaded themselves in a synagogue and attacked security forces.
Amona residents announced they would begin a hunger strike on Wednesday until the government kept its commitment to build them a new settlement.
The Palestinian information ministry denounced what it said was a media stunt.
"Nine houses are destroyed in exchange for thousands of others built," it said.
In the days after Trump entered the White House, Israel announced more than 5,000 new homes in settlements in east Jerusalem and the occupied West Bank.
The government also backed a bill passed by parliament earlier this month legalising dozens of other settlements that even Israel previously considered illegal.
The United Nations said the law crossed a "red line" towards the annexation of the West Bank, but the United States chose not to condemn the move.
Most of the international community sees settlements as a major obstacle to peace, as they are built on land the Palestinians see as part of their future state.
Israel distinguishes between settlements it has authorised and those built without permission. The demolition of Amona, just a few hundred metres from Ofra, became a major political story.
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