Washington • Plagued with an inadequate health care system and fearful of what could happen if the coronavirus spread across its tribal lands in South Dakota, the Cheyenne River Sioux Tribe took emergency steps 12 weeks ago, setting up checkpoints along roads into its reservation to question travelers about their health and their travel plans.

Gov. Kristi Noem, a Republican, objected, saying the checkpoints amounted to an unlawful infringement on state and federal power and threatening legal action against the tribe if they were not removed. When the tribe would not back down, crediting the checkpoints with keeping cases to half a dozen, she appealed for help from President Donald Trump and the White House, as well as the state’s congressional delegation.

But once Mark Meadows, the White House chief of staff, tried to broker a solution, tribal officials interpreted it as an implicit threat to jeopardize their portion of coronavirus relief aid. Tensions were further inflamed when top Interior Department officials in charge of tribal affairs began threatening to withhold federal funding for the tribe’s police force, the tribe said, a step tribal leaders took as a challenge to their sovereignty on their land.

Now the standoff is moving to the courts. On Tuesday, the tribe filed suit in U.S. District Court in Washington asking a judge to prevent the administration and state officials from closing the checkpoints and withdrawing funding from the tribe.

It is the latest effort by tribal governments to draw attention to the deep-rooted problems in their relationship with the federal government, including underfunded assistance programs and long-standing issues with the availability and quality of care provided by the Indian Health Service. The facility that serves the Cheyenne River Sioux Tribe, according to the lawsuit, has only eight inpatient beds and six ventilators for the tribe’s 10,000 residential members.

The pandemic, which has devastated tribes across the country, has only aggravated the systemic disparities, prompting a series of legal challenges over how the federal government has administered aid and assistance.

In seeking to end the tribe’s use of checkpoints, the administration is “forcing us to accept contagion into our community when we have exercised our sovereignty in a way that benefits our community,” said Nikki Ducheneaux, a member of the Cheyenne River Sioux Tribe and one of the lawyers representing the tribe in the court case.

The Interior Department and Noem did not respond to requests for comment.

A spokesman for the White House, Judd Deere, said the administration had provided “unprecedented support to the American Indian community,” including $8 billion to address preparedness, response and recovery through the $2.2 trillion stimulus law. “The Trump administration has also delivered 250 Abbott testing systems to the Indian Health Services and tribal health care facilities for distribution,” he said in a statement.

The tribe, in one of the poorest counties in the country, first established the health checkpoints in early April, hoping to avoid the skyrocketing number of coronavirus cases that have afflicted other tribes. The infection and death rates among some tribes, including the Navajo Nation, are among the highest in the country, and Native Americans account for 13% of cases in South Dakota, according to data from the state’s Health Department.

The checkpoints include a questionnaire about where travelers are coming from and their destination. The tribe then uses the state Health Department’s website, which tracks community spread and hot spots, to determine whether to allow entry onto the reservation. Only six people have tested positive for the virus, and tribal officials credit the checkpoints for helping them track cases and any spread, said Remi Bald Eagle, the intergovernmental affairs coordinator for the Cheyenne River Sioux Tribe.

Bald Eagle said the health checkpoints had been crucial to minimizing the number of positive cases on the reservation, particularly given the lack of a statewide stay-at-home order. Last month, with the support of tribal leaders, the state of New Mexico blocked roads leading into the city of Gallup, on the edge of the Navajo Nation, in an effort to restrict the spread of the virus.

“We will not apologize for being an island of safety in a sea of uncertainty and death,” the tribe wrote in its lawsuit, which names Trump, Meadows, and other top White House and Interior Department officials.

Noem called in May for all tribes in South Dakota to end the checkpoints and “cease interfering with or regulating traffic,” threatening legal action if they were not removed and citing instances where nontribal residents struggled to pass through the reservation on state and federal highways.

The tribe contends that its sovereignty allows them to keep the checkpoints running and to operate them on the state and federal highways, one of its main points of dispute with Noem.

“This, however, is not simply a matter between a sovereign state and a sovereign tribal government,” Noem wrote in a letter to Trump. “The federal government has an interest in interstate commerce, transportation of critical infrastructure goods, provision of services from critical infrastructure industries and the uniform treatment of all travelers.”

Meadows, who represented some tribal governments while serving as a member of Congress from North Carolina, personally reached out in June to the tribe’s chairman, Harold Frazier, according to the lawsuit and phone transcripts obtained by The New York Times. He implored the chairman to reach a solution with state officials. “I can’t have checkpoints by individuals on federal highways,” he said, according to the transcript, before raising the $8 billion pot set aside for tribes in the stimulus law.

“I also need you to use that money so that it doesn’t create a problem for me on other issues because we still have another 40% of the money to go out,” Meadows said, phrasing that the tribe said in the lawsuit amounted to “threatening the security” of the federal aid. (Ducheneaux said that the tribe received a portion of the aid but that the Treasury Department could audit the expenditure of those funds.)

In ensuing calls, Frazier, the head of the tribal government, spoke with a number of federal officials including Dr. Deborah Birx, the coronavirus response coordinator, who suggested providing more testing to the tribe as a way to reduce the need for the checkpoints.

The impasse, the tribe said in the suit, further escalated when administration officials inspected the checkpoints and raised concerns about the officials conducting the inspections, saying they were violating the law that allows the tribe to use federal aid to hire its own law enforcement officials.

“It is not in the best interest of the tribe, state, or federal government to have individuals falsely representing themselves as law enforcement, as proper training, background investigations and other protocols should be followed to ensure public safety,” a spokesman for the Bureau of Indian Affairs said in a statement.

Tara Sweeney, the top official at the bureau, wrote to the tribe demanding closure of the checkpoints if the tribe wanted to maintain that funding. The staff monitoring the checkpoints are not funded using that pot of federal money, according to the lawsuit.