KAYENTA, Ariz. — The world’s largest coal company, Peabody Energy, is seeking federal approval to expand its mine on Navajo and Hopi land in northern Arizona, a move supported by tribal leaders. But many other tribe members say the expansion would destroy burial grounds and pre-Columbian ruins and are opposing it in court.

The dispute is the latest episode in a series of longstanding conflicts involving the treatment of Native American ancestral lands, mining companies and the federal government. Like the Dakota Access oil pipeline project, the Kayenta mine dispute pits the rights of tribes against powerful industry and federal interests.

Peabody built its first mine on this coal-darkened plateau 50 years ago, and in the process dug up an adjacent American Indian village. The dig uncovered an “enormous body of knowledge” about ancient Indian tribes who flourished here three millenniums ago, according to Beth Sutton, a Peabody spokeswoman.

But Leland Grass, a Navajo horse trainer, called the dig a “desecration.” He and other tribe members complained that Peabody handed off 192 sets of human remains to an anthropology professor, destroyed ancient petroglyphs and archaeological ruins, and warehoused 1.2 million artifacts at Southern Illinois University, which helped conduct the dig.

Unlike the pipeline project at Standing Rock, however, Peabody’s mine plan has the backing of the official tribal governments because the original mine is one of the few sources of jobs and revenue on the impoverished reservations. Peabody has paid about $50 million per year to the Navajo and Hopi tribes since 1987, according to a federal report released in 2012, because the mine was built on tribal land.

But several powerful Navajo nongovernmental organizations, at odds with their leaders, have joined with the Sierra Club to try to curb the mine expansion, arguing that the mine harms air and water quality and that Peabody’s initial plan did not include enough protections for so-called cultural resources like graves. While they acknowledge that they cannot stop the mine project, they at least want Peabody and the government to protect ceremonial sites, ruins and graves in the expanding mine’s path.

To that end, these groups have brought a lawsuit that has forced the government to undertake a Preservation Act study to identify burial grounds and sites of archaeological importance. For projects on or near tribal land, the government must consult with tribes.

The problem, however, say tribal activists and preservation law experts, is that the permitting system…