After months of inaction on the Dakota Access pipeline protest, the Obama administration has put itself at odds with the Standing Rock Sioux by giving protesters 10 days to vacate the camps illegally located on federal land.

In a Friday letter posted online, the U.S. Army Corps of Engineers asked Standing Rock Sioux chairman David Archambault II to “encourage” tribal members and others to end their illegal occupation of federal property north of the Cannonball River by Dec. 5.

At the same time, Col. John W. Henderson said the protesters, who number as many as 3,000, are welcome to remain in the “free speech zone” south of the Cannonball River, which is also under federal jurisdiction, or move elsewhere.

Any activists found on the federal property after Dec. 5 “may be subject to prosecution under federal, state and local laws,” he said.

Mr. Archambault responded Friday by doubling down on the tribe’s opposition to the Dakota Access pipeline, saying the tribe is “deeply disappointed by the United States, but our resolve to protect our water is stronger than ever.”

“The best way to protect people during the winter, and reduce the risk of conflict between water protectors and militarized police, is to deny the easement for the Oahe crossing, and deny it now,” said Mr. Archambault.

He did not say whether he would comply with the Corps’ request.

Local authorities have made about 530 arrests since Aug. 1 as foes of the Dakota Access pipeline flood the rural area with protest activity, clashing repeatedly with law enforcement in an effort to stop the $3.8 billion, 1,172-mile project.

The tribe has called for the Corps of Engineers to cancel a previously issued permit on the pipeline’s final 1,100 feet in North Dakota over concerns about water quality and historic relics. The four-state project is 87 percent complete.

In his letter, Mr. Henderson said he was “genuinely concerned for the safety and well-being of both the members of your Tribe and the general public located at these encampments.”

The protesters are now committing a number of violations, including “unauthorized structures, fires, improper disposal of waste, and camping,” he said.

“Additionally, any tribal government that sponsors such illegal activity is assuming the risk for those persons who remain on these lands,” Mr. Henderson said in the letter.

Still unclear is whether the agency plans to bring in federal marshals to enter the camps and remove the protesters if they refuse to leave by Monday.

The local sheriffs’ departments have focused their limited resources on keeping the activists from holding demonstrations on private land and blocking public highways and streets, not on enforcing code violations within the camps.

Whether the tribe is capable of clearing the protesters is also in question, given that a militant cohort of activists have ignored repeated pleas from Mr. Archambault to conduct themselves “peacefully and prayerfully.”

The tribal council voted Nov. 1 to ask the aggressive Red Warrior Camp to leave, but its members are still encamped on the federal property, according to local authorities.

Rob Port, a North Dakota-based conservative radio talk-show host who runs the Say Anything blog, warned that the occupiers may well put up a fight.

“The #NoDAPL folks aren’t likely to go quietly. I mean, they’ve been building permanent structures on Corps Land, which the Corps specifically forbid in their special use permit allowing the protest camp,” Mr. Port said on his blog.

He noted that so far “the feds have largely withheld law enforcement support.”

“Are they expecting North Dakota cops to clear the protesters off federal land?” he asked. “Or are the feds finally getting in the game? Either way, I don’t think the camp is going to be closed down peacefully. I hope I’m wrong.”

In his statement, Mr. Archambault also accused the Corps of being “disrespectful” by issuing the request a day after Thanksgiving, “a historic exchange of goodwill between Native Americans and the first immigrants from Europe.”

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