Ambulance workers told the Agence France Presse (AFP) news service that around 250 people were injured in the operation, with two said to be in a serious condition.
Among the hurt, two ultranationalist members of parliament, Arieh Eldad and former cabinet minister, Efi Eitam.
In a telephone interview from the scene of the confrontation, Mr Eldad told Israel Radio that police were “treating people here like the Arabs.”
It is the first forced removal of Jewish settlers from Palestinian territory since the mass pullout from Gaza and parts of the West Bank last August.
Around 2,000 defiant settlers had gathered at the Amona outpost in a bid to thwart the evacuation order which had been cleared by the Israeli Supreme Court in the morning.
But they were outnumbered by police and troops who assembled in riot gear and brought in horses and heavy machinery to break through hastily erected barricades.
About an hour into the operation, police reached the first of nine homes marked for demolition and began tearing through window shutters with a crowbar.
Protesters were dragged through the windows as settlers hurled rocks, paint balloons and eggs from the rooftop above.
Some troops rode to the tops of roofs in the shovels of bulldozers and then forced settlers into the shovels to bring them down.
Protesters resorted to using wooden stakes in an attempt to fend off soldiers and set fire to tyres along the rooftops.
After four hours, the last of the settlers had been taken from the houses which were then reduced to rubble by mechanical diggers.
Acting Prime Minister Ehud Olmert, who ordered the evacuation, said the protesters had crossed the bounds of acceptable behaviour.
“This is a phenomenon that cannot continue or be accepted. When bricks are thrown at the heads of soldiers and police officers, a line has clearly been crossed,” he was quoted as saying at a parliamentary committee meeting.
“This is reaching a scope we haven’t seen before. This was an organised activity on the part of the settlers for political ends.”
But this fierce resistance may be something that is seen again.
If Mr Olmert steps into the post of Prime Minister after the March general election, he is widely expected to call for the evacuation of settlements of the West Bank.
Dozens of wildcat Jewish enclaves, such as Amona, have mushroomed in the West Bank since the mid- 1990s.
Many settlers feel betrayed by the evacuations as Israeli Prime Minister Ariel Sharon, who remains in a coma, had previously encouraged them to “seize the hills” and set up homes.
“It was Ariel Sharon who called on us to come here and now they are expelling us from our homes,” said 33- year- old Sarah Franck, one of Amona’s residents.
Under the internationally- backed ‘road map’ peace plan, Israel has committed to dismantling about two dozen rogue settlements, but so far has taken little action.