Protest organiser Mekasi Camp-Horinek said after he and his mother were arrested, police placed them in one of the metal enclosures together and wrote a number on his arm. He told the Los Angeles Times that there was no bedding or furniture in the cage.
"It goes back to concentration camp days," Camp-Horinek said.
The Morton County Sheriff's Department said in a statement that the enclosures were "temporary holding cells" made out of chain link fence and were only used when police made mass arrests, as was the case on Friday.
The cells are approved by the North Dakota Department of Corrections, and prisoners have access to bathrooms, meals and drinking water, the department said. The Morton County Correctional Centre, where many of the prisoners were transported, has room for 42 inmates at a time.
Morton County spokesman Rob Keller told the Bismarck Tribune that police used numbers to keep track of personal property when they were released from jail.
The 1885km pipeline is slated to carry oil from North Dakota through the Midwest to Illinois, where it can be sent to refineries. The Standing Rock Sioux and other Native American tribes say a portion of the pipeline threatens to pollute their only drinking water supplies and disrupt cultural lands. Energy Transfer Partners, the developer, and North Dakota officials say the pipeline is safe and would not harm cultural sites.
For months, activists have used a camp on federally owned land to stage demonstrations against the US$3.8 billion project, which is close to completion in North Dakota. Last week, some protesters attempted to set up another encampment on private property nearby, using vehicles, scrap wood and bales of hay to barricade roadways in the area.
Authorities moved in with trucks and military Humvees when protesters refused to leave, using pepper spray, rubber bullets and high-pitched noise cannons to disperse the crowd of several hundred. Some protesters set fires along the road and threw rocks and Molotov cocktails at authorities, while others on the scene prayed and passively resisted.
During the confrontation, one protester allegedly opened fire on sheriff's deputies, nearly striking one, authorities said. The suspect, Red Fawn Fallis, was arrested and charged with attempted murder.
Police took 141 protesters into custody, according to the sheriff's office.
On Sunday, all of them walked free when an anonymous donor paid US$2.5 million to have them released, News On 6 reported.
Tribal leaders have criticised the response from law enforcement, saying more than 40 people were injured by pepper spray and bean bag rounds fired by authorities while others were humiliated by their treatment while in custody. Standing Rock Sioux Chairman Dave Archambault II said he is considering a class-action lawsuit against law enforcement, the Bismarck Tribune reported.
"The best way for success is to go after every individual law enforcement who fired a weapon at innocent people," he said. "We have to get badge numbers. We have to get facial recognition. We have to get these law enforcement that are from other states, whoever it is. And individuals who are harmed have to report what has happened."
Archambault has also called for the US Department of Justice to investigate the tactics used by authorities.
"DOJ can no longer ignore our requests," Archambault said. "If harm comes to any who come here to stand in solidarity with us, it is on their watch."
Cheyenne River Sioux Chairman Harold Frazier said he was alarmed when he found out people were marked with numbers after being arrested.
"It's really sad," he said. "Their rights obviously have been violated."
