The Environmental Protection Agency's inspector general is examining the agency's failure to adequately measure potentially toxic air emissions from the nation's factory farms, a lapse that environmental groups say has allowed livestock operations to spew air pollution without government oversight for more than a decade.

Air emissions from livestock facilities—including larger farms known as concentrated animal feeding operations, or CAFOs—can fall under three separate federal laws if the pollution they emit hits certain thresholds. But the government and livestock industry have struggled to agree on accurate ways of measuring those emissions, so livestock facilities have largely escaped government scrutiny.

Nearly a dozen years ago, the Environmental Protection Agency said it would develop a way to measure emissions from feeding operations. But it still hasn't completed the process, prompting the EPA's Office of Inspector General—the agency's internal watchdog—to launch an investigation this year to determine why.

"The agency is reluctant to regulate agriculture and it's a big problem in the eyes of the inspector general," said Brent Newell, an attorney with the Center for Race, Poverty and the Environment, which has sued the agency to regulate livestock facilities. "They're not exempt from these laws."

The Inspector General (IG) is stepping in because progress has stalled on a 2005 deal known as the Air Compliance Agreement between the EPA and factory farms. Under it, those farms were exempt from air emissions violations, but in exchange, the farms allowed the EPA to measure air emissions so the agency could gather data that would allow it to eventually set standards for air pollution.

"The government had no data," said Michael Formica, an attorney with the National Pork Producers Council. "That's when we said: 'Let's do a study.'"

A report on the investigation is expected next spring, regardless of the change in administration, but President-elect Donald Trump has vowed to roll back environmental regulations, not expand them, and he has a Republican Congress as his ally. Typically, after the Inspector General issues its report, the agency replies with an action plan to address the problem. It seems unlikely that a Trump EPA would respond.

"I don't think the agency's response necessarily creates any mandatory obligations," explained Tarah Heinzen, an attorney with Food and Water Watch, an advocacy group that has petitioned the agency to regulate air emissions. "I also suspect the next Congress won't be too upset if EPA continues not to act to address CAFO emissions."

Over the past three decades, the number of CAFOs in the U.S. has skyrocketed from about 3,600 in the early 1980s to more than 19,000 today. As livestock production has become increasingly industrialized, environmental groups have called for the government to regulate CAFOs as it has other industries.

Environmental groups' main concern has been water pollution, which falls under the Clean Water Act. But communities near CAFOs have complained for years about their stench, as well as the health and ecological impacts of emissions of ammonia, hydrogen sulfide, particulates and other contaminants. More recently, CAFOS have come under scrutiny for emissions of methane and nitrous oxide, linked to global climate change.

"The EPA has put in regulation on oil and gas, and proposed regulations on landfills, but they've done nothing on CAFOs," said Jonathan Lovvorn, an attorney with the Humane Society of the United States, which has petitioned the agency to regulate CAFOs under the Clean Air Act. "So when we're looking at the goals for the Paris agreement, this is a huge leak in the safety net. They've done nothing on this."

Measuring emissions from livestock facilities, though, is more difficult than measuring them from other sources. Compounding the problem, the agency has little idea where many of these facilities are located.

"They're trying to suggest you can regulate them like you can from any other [industry]," said Formica of the National Pork Producers Council. "You can't. Each farm is different. It depends on the health of the animal, the temperature, what type of animal, the region."

Environmental groups agree—to an extent. "There's a kernel of truth to that," said Eve Gartner, an attorney with the advocacy group Earthjustice, which has sued the agency for exempting CAFOs from federal law. "It's a little harder to monitor what's coming out of a CAFO. There's not a stack."

Air emissions from CAFOs can fall under the federal Clean Air Act. They can also fall under the Comprehensive Environmental Response, Compensation, and Liability Act, often referred to as CERCLA or the Superfund law, and the Emergency Planning and Community Right-to-Know Act, or EPCRA. The latter two are "right-to-know" laws, rather than regulatory laws, but in all three, the laws only kick in when emissions meet certain thresholds.

Momentum to tackle the issue gathered in the 1990s, leading to the Air Compliance Agreement in 2005.

Under it, the, EPA approved nearly 2,600 agreements, representing 14,000 farms, which critics call a free pass to pollute for most of the CAFOs in the country.

"So many industries have emissions [measurements], and they don't have to be perfect," Heinzen said. "For the EPA to make perfect the enemy of the good here—to me it's just another example of agricultural exceptionalism."

In 2008, the EPA responded to a request by the poultry industry by issuing a rule not only exempting poultry facilities from reporting leaks of ammonia, hydrogen sulfides and other hazardous substances, but also all large livestock facilities, under the Superfund law. The agency exempted all but the largest feeding operations from reporting releases under EPCRA.

The Government Accountability Office questioned this exemption in a 2008 report and environmental groups challenged the rule in court. The government responded by sending the rule back to the EPA, which has not modified the rule, so the exemption still stands.

The EPA did release its study of emissions in 2011, but it modeled information from only 25 farms and the results were immediately discounted by the agency's own Science Advisory Board as useless beyond those 25 farms.

Environmental groups have vowed to keep up the pressure.

A coalition of groups, led by the Humane Society of the United States, filed a petition with the EPA in 2009, asking it to regulate CAFOs under the Clean Air Act as "stationary sources" of emissions. In 2011, another coalition asked EPA to set health-based standards for ammonia.

In early 2015, the coalitions sued the the agency for failing to act on the petitions, but the U.S. District Court for the District of Columbia dismissed the lawsuits on a technicality.

The groups have said they will refile those suits within the next six months, and the Inspector General's report should have been issued by then as well. But with a new administration well underway at that point, the groups say they are skeptical the agency will make any progress toward regulating air pollution from the country's livestock farms.