WASHINGTON — Holding a job unlawfully is not a reason to be fired in the Trump administration.

Last month, a Montana judge ruled that the acting head of the Bureau of Land Management, which holds sway over millions of acres of federal land, should be removed from his position because he was performing his duties illegally. The Interior Department’s response? Tweak his title.

Since March, William Perry Pendley is the third high-ranking administration official that the courts have found likely to be working in violation of the Federal Vacancies Reform Act, a 1998 law governing how a president may appoint temporary officials. Such findings have been bolstered by the Government Accountability Office and other agencies.

In each case the administration has responded with defiance.

“We depend on an administration’s willingness to comply with the law, including judicial orders, findings of independent agencies, and congressional demands for information,” said Kathleen Clark, a government ethics expert at Washington University in St. Louis. “The Trump administration discovered it had a secret superpower, which was that it could fail to comply basically without consequences.”

If the trend continues into a second term for President Trump, government watchdogs said, it could entangle policies, on everything from immigration to land management, in lengthy legal tussles. Mr. Trump’s recent hospitalization after testing positive for the coronavirus moved the question of just who is in charge of the government front and center.

Farther down the leadership chain, the president’s penchant for filling high-level jobs without Senate confirmation was causing confusion long before the coronavirus pandemic.

“Confirmation hearings in the Senate are really important,” said Peter Jenkins, senior counsel for the Public Employees for Environmental Responsibility.

“If they pass and get enough votes, it means they’re mainstream enough to satisfy both sides,” Mr. Jenkins said. By consistently bypassing the law, he said, “You get lower level, unqualified or fringe characters running the bureaus. The employee morale suffers, the performance of the agencies declines and the resources suffer.”

Mr. Cuccinelli is now the acting Deputy Secretary of Homeland Security.

A different federal judge in Maryland later ruled that Chad F. Wolf is “likely” serving unlawfully as acting secretary of the Department of Homeland Security, a conclusion the Government Accountability Office had arrived at in August. The court temporarily barred the Trump administration from enforcing new directives Mr. Cuccinelli and Mr. Wolf had issued imposing restrictions on asylum seekers.

But both men remain in their positions.

In the case of the Bureau of Land Management, the ruling was definitive. Late last month, Brian Morris of the United States District Court for the District of Montana, who was appointed under the Obama administration, found that Mr. Pendley had served unlawfully for 424 days as acting director of the bureau.

Any function or duty Mr. Pendley performed during that time, Judge Morris ruled, “would have no force and effect and must be set aside as arbitrary and capricious.”

He ordered briefs from all parties regarding which of Mr. Pendley’s policies should be overturned, due this week.

Mr. Pendley, a former oil-industry lawyer, has ridiculed the established science of climate change and called for the sale of public lands. He has led the agency since August 2019 as “deputy director for programs and policy,” a title that David Bernhardt, the Interior secretary, augmented with, “exercising the authority of director.”

The White House formally withdrew his nomination in August, a tacit acknowledgment that he could not win Senate confirmation.

Under Mr. Pendley the bureau has approved dozens of land management plans and expanded oil and gas drilling in several states, including within the Bears Ears and Grand Staircase Escalante national monuments in Utah. He also has spearheaded moving the bureau from Washington, D.C., to Grand Junction, Colo., which many environmental groups believe is part of an effort to hollow out the agency.

The Department of Interior has vowed to appeal Judge Morris’s order.

“Consistent with the law, Secretary Bernhardt will continue to lead the Department and all of its bureaus, including the Bureau of Land Management,” the Interior Department’s solicitor general, Daniel Jorjani, said in a statement. “In so doing, he will continue to rely on the Bureau of Land Management’s superior management team, specifically including Deputy Director for Programs and Policy William Perry Pendley, who will continue to serve in his leadership role at the Bureau of Land Management.”

The bureau subsequently removed “exercising the authority of director” from Mr. Pendley’s title on its organization chart. When asked about the change, the agency did not respond to a request to explain the change.

The Federal Vacancies Reform Act bars acting agency officials from serving for more than 210 days without Senate confirmation. According to the Government Accountability Office, there were six violations of the act during the eight years of the Obama administration and eight so far during the Trump administration’s first term.

The Constitutional Accountability Center, a liberal research group, has identified 15 high-ranking Trump administration officials who are currently holding jobs in violation of the vacancies act.

Lisa Heinzerling, a professor of environmental and administrative law at Georgetown University, called keeping Mr. Pendley in his leadership role a “level of recalcitrance about a judge’s opinion that is striking.”

In the case of officials serving in violation of the Federal Vacancies Reform Act, Mr. Trump’s own agenda could be at stake, since decisions made by officials with legally questionable authority could be challenged in court.

Environmental groups have argued that the court ruling effectively nullifies any official public land management decisions made by Mr. Pendley or the Bureau of Land Management during his tenure.

“Every single decision Pendley has signed off on is now in legal jeopardy,” said Senator Tom Udall of New Mexico, the top Democrat on the Senate appropriations subcommittee with oversight of the Interior department. He accused the Trump administration of being willing to “flout the law” to keep Mr. Pendley

Gov. Steve Bullock of Montana, who filed the lawsuit to block Mr. Pendley from serving as head of the bureau, intends to file this week a list of “significant” decisions that he believes can now be considered unlawful, a spokeswoman for the governor said.

In a statement, Gov. Bullock said the court was clear that Mr. Pendley cannot continue to lead the bureau, “regardless of what the agency puts on his business card this month.”