The Trump administration gutted protections for migratory birds on Tuesday, delivering the second of two parting gifts to the oil and gas industry, which has long sought to be shielded from liability for killing birds unintentionally in oil spills, toxic waste ponds and other environmental disasters.

The move, by the Department of the Interior, came a day after the Environmental Protection Agency finalized another regulation that had long been sought by fossil fuel companies and other major polluting industries: A measure that effectively bars some scientific studies from consideration when the agency is drafting public health rules.

The two regulations are among the last major environmental rollbacks expected from the Trump administration and will present an immediate challenge to the incoming Biden administration, which has pledged to suspend and reverse many of the last-minute rules known as midnight regulations.

“These are definitely midnight regulations,” said Richard Revesz, an environmental law professor at New York University. “They’re 11:59 and 59 seconds regulations.”

A senior official with the Biden transition team, speaking on background Tuesday in a briefing call with reporters, called the last-minute rollbacks an “unrelenting assault” on the environment and said rebuilding federal agencies that the Trump administration has gutted will be an enormous task. The official vowed the policies would be reversed, but when and how long that might take may depend on several factors, including when the measures go into effect.

“One way or another the most pernicious of these rules will end up getting undone,” Mr. Revesz said. But he and other legal experts said reversing the measures would not be a quick or easy process.

In the case of the bird rule, conservationists and oil industry executives alike have said that was precisely what the Trump administration intended. The industry has long sought to be shielded from liability for killing birds unintentionally in oil spills, toxic waste ponds and other environmental disasters.

Under the measure, which changes the way the 1918 Migratory Bird Treaty Act is implemented, the federal government will no longer fine or prosecute companies whose actions cause the death of birds, as long as killing birds was not the underlying intent of the action. That holds true for accidents like oil spills and electrocutions on power lines — and also intentional or even illegal acts, like the spraying of a banned pesticide — as long as birds are not the intended target of the poison.

David Bernhardt, the interior secretary, described the new policy as a simple clarification of the law.

“This rule simply reaffirms the original meaning and intent of the Migratory Bird Treaty Act by making it clear that the U.S. Fish and Wildlife Service will not prosecute landowners, industry and other individuals for accidentally killing a migratory bird,” Mr. Bernhardt said in a statement.

Industry leaders and administration officials said they expected businesses to continue to voluntarily protect bird habitats. They have said that removing the threat of punishment would eliminate legal disputes about the law’s intent and bring regulatory certainty to companies worried that bird deaths would make them criminally liable for millions of dollars.

“Our industry is committed to the protection of migratory birds,” Amy Emmert, a senior policy adviser for the American Petroleum Institute, said in a statement. She described the new rule as “modernized” and said it “reinforces the original intent of the Migratory Bird Treaty Act and accounts for the fact that the natural gas and oil industry is not a primary threat to bird populations.”

Environmentalists called the decision cruel.

“It’s horrendous,” said Eric Glitzenstein, director of litigation at the Center for Biological Diversity, an environmental group. “It will just have a really overwhelming negative effect on our already dwindling bird populations.”

The Migratory Bird Treaty Act was originally enacted to protect birds from poaching and over-hunting. It makes it illegal “by any means or in any manner” to hunt, take, capture or kill birds, nests or eggs from listed species without a permit.

Accidentally killing birds is rarely prosecuted under the law, but there have been notable exceptions, like when the Obama administration prosecuted seven oil companies in North Dakota for the deaths of 28 birds.

The Migratory Bird Treaty Act was also part of the basis for a $100 million settlement with BP for the deaths of more than one million birds in the 2010 Deepwater Horizon spill. And, in 2009, Exxon Mobil paid $600,000 after pleading guilty in the deaths of protected owls, raptors and waterfowl that died in uncovered natural gas pits, oil tanks and wastewater facilities.

Activists said that just the possibility of penalties has helped push industry to take precautions to prevent bird deaths. By announcing that protected birds can be legally killed as long as killing birds isn’t the goal, some said, they worried that the federal government would effectively be removing incentives for companies to take measures to protect birds.

In fact, the Trump administration recently acknowledged as much. An environmental-impact statement issued in late November by the United States Fish and Wildlife Service said that without the inducement of law, industry could be expected to scale back on voluntary bird protections.

Sarah Greenberger, vice president of conservation at the Audubon Society, noted that the Trump administration’s move came just as the organization’s 121st annual bird census, known as the Audubon Christmas Bird Count, was underway. In 2019, she said, despite record participation, 6 million fewer birds were counted.

“While we don’t yet know exactly what caused this decrease, it comes amid new science showing alarming trends in bird declines, like the loss of 3 billion birds in North America since 1970,” she said.

Mr. Glitzenstein said his group and others were planning to challenge the rule in court even as they push the incoming Biden administration to reverse course. A federal judge in August rejected the Trump administration’s legal rationale for the regulation.

The E.P.A. regulation, known as the Strengthening Transparency in Pivotal Science Underlying Significant Regulatory Actions and Influential Scientific Information Rule, says that “pivotal” scientific studies that make public their underlying data and models must be given more weight than studies that keep such data confidential. The agency concluded that the E.P.A. or anyone else should be able to independently validate research that impacts regulations.

“It’s sunshine, it’s transparency,” Andrew Wheeler, the administrator of the E.P.A., said of the regulation on Tuesday during an online forum with the Competitive Enterprise Institute, a free-market think tank that opposes most environmental regulation. He described the policy as an effort “to reduce misunderstanding of our regulatory decisions.”

Yet thousands of public health experts, scientific groups and medical organizations objected to the rule contending it is actually designed to block the use of studies that prove the links between increased exposure to toxic substances and impaired health in order to avoid new regulations.

The rule downgrades the use of population studies in which subjects offer medical histories, lifestyle information and other personal data only on the condition of privacy. Such studies have served as the scientific underpinnings of some of the most important clean air and water regulations of the past half century.

Critics say the agency’s leaders disregarded the E.P.A.’s scientific review system to create an additional layer of scrutiny designed to impede or block access to the best available science, weakening the government’s ability to create new protections against pollution, pesticides, and possibly even the coronavirus.

“Right now we’re in the grips of a serious public health crisis due to a deadly respiratory virus, and there’s evidence showing that air pollution exposure increases the risk of worse outcomes,” said Dr. Mary Rice, a pulmonary and critical care physician who is chairwoman of the environmental health policy committee at the American Thoracic Society.

“We would want E.P.A. going forward to make decisions about air quality using all available evidence, not just putting arbitrary limits on what it will consider,” she said.

The E.P.A. policy goes into effect immediately under an unusual procedural tactic that allows the administration to avoid a traditional 30-day waiting period after a regulation appears in the federal register. Doing so could prevent the Biden administration from immediately suspending the regulation.