Dozens of youths exchanged blows with about 50 soldiers on Wednesday as other young settlers rushed to the scene to help their comrades.
Soldiers restrained the activists and dragged several through the sand into a waiting army vehicle. There were no immediate reports of injuries.
The settlers established the outpost earlier this week after Israeli troops demolished 11 nearby buildings.
Israeli soldiers removed several dozen Jewish activists from a Palestinian house in Gaza at sunset on Wednesday, witnesses said, arresting many of the squatters, who oppose Israel's planned pullout from Gaza.
Day of violence
The soldiers moved in after a day of violence at the site in Shirat Hayam.
The Jewish activists threw rocks at Palestinians and scuffled with soldiers, and Palestinians threw rocks at the Israelis, in the most serious clash since Israel announced its plan to vacate Gaza.
Israeli troops moved into Gaza's
Shirat Hayam to prevent clashes
One Palestinian was in critical condition.
The authorities had feared that opponents of Israel's planned withdrawal from the Gaza Strip would use the buildings as centres of resistance during the evacuation, set to begin in mid-August.
Occupants of the colony clashed with local Palestinian residents on Tuesday, with both sides throwing rocks.
The army said it moved into the area on Wednesday to arrest some of the Israeli stone throwers. Israeli media said five people were arrested.
The army added that Israeli police were also participating in Wednesday's operation, but a police spokeswoman had no information on it.