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CANNON BALL, N.D. — Authorities on Thursday cleared a protest camp where opponents of the Dakota Access oil pipeline had gathered for the better part of a year, searching tents and huts and arresting three dozen holdouts who had defied a government order to leave.

It took 3½ hours for about 220 officers and 18 National Guard members to methodically search the protesters’ temporary homes and arrest people, including a man who climbed atop a building and stayed there for more than an hour before surrendering.

Native Americans who oppose the $3.8 billion pipeline established the Oceti Sakowin camp last April on federal land near the Standing Rock Indian Reservation to draw attention to their concerns that the project will hurt the environment and sacred sites — a charge that Dallas-based pipeline developer Energy Transfer Partners disputes. The camp gained increased attention starting in August after its population had grown and authorities made their first arrests. At its height, the camp included thousands of people, but the numbers had dwindled during the winter and as the fight over the pipeline moved into the courts.

The Army Corps of Engineers said it needed to clear the camp ahead of spring flooding, and had ordered everyone to leave by 2 p.m. Wednesday. The agency said it was concerned about protesters’ safety and about the environmental effects of tents, cars, garbage, and other items in the camp being washed into nearby rivers.

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Most protesters left peacefully Wednesday when authorities closed the camp, but some stayed overnight in defiance of the government order.

As police in full riot gear worked to arrest the stragglers Thursday, cleanup crews began razing buildings on the square-mile piece of property at the confluence of the Cannonball and Missouri rivers.

Authorities chose to enter the camp ‘‘cautiously and tactfully’’ to ensure the safety of both officers and protesters, according to Highway Patrol Lieutenant Tom Iverson. The arrests were a last resort, he said.

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‘‘We did not want this. Unfortunately, there were some bad actors that forced us into this position,’’ he said.

Only one person resisted arrest; otherwise there were no major incidents and there were no injuries, Morton County Sheriff Kyle Kirchmeier said.

Energy Transfer Partners began work on the last big section of the oil pipeline this month after the Army gave it permission to lay pipe under a reservoir on the Missouri River. When complete, the pipeline will carry oil through the Dakotas and Iowa to a shipping point in Illinois.