Environmental Protection Agency (EPA) Administrator Lisa Jackson. The EPA finalized rules late Thursday to curb pollution from industrial boilers and cement plants. (Kevin Wolf/AP)

The Environmental Protection Agency finalized rules late Thursday to curb pollution from industrial boilers and cement plants, agreeing to give industry additional time for compliance and easing some emissions limits from earlier proposals.

The new rules, which have been enmeshed in a fierce regulatory and legal fight for more than a decade, drew criticism from environmentalists.

Earthjustice staff attorney James Pew, who fought earlier versions in federal court, called the set of rules “an avalanche of bad news.”

For the first time, large boilers and cement kilns will face strict limits on mercury, acid gases and fine particulate matter, or soot. But the EPA will give boiler owners three years to meet the new standards, with a possible extension for another year after that, meaning they would take effect in 2016 at the earliest. Cement plants will not have to comply with the new limits until September 2015, two years after they were originally set to take place.

There are fewer than 115 cement plants in the United States, but they account for 7 percent of the mercury released into the air from stationary sources.

Mercury contamination gets into the food chain when it enters waterways and soil in the form of precipitation, and it can cause neurological damage in infants and young children.

Although the most restrictive limits will affect just 1 percent of the nation’s nearly 1.5 million boilers, industry had fought restrictions in the past because these facilities are integral to the operations of hospitals, paper plants and factories.

Boiler operators had sought to delay the rules by five years, until 2018.

The measures will deliver significant health benefits and impose major costs on the U.S. manufacturing sector. Meeting the standards for boilers and some incinerators will cost industry between $1.3 billion and $1.5 billion annually, the EPA estimates, and is expected to avoid up to 8,100 premature deaths, prevent 5,100 heart attacks and avert 52,000 asthma attacks each year once fully implemented.

The annual cost of the cement rules will run a few hundred million dollars, according to the agency, while delivering billions annually in health benefits.

Donna Harman, president and chief executive of the American Forest and Paper Association, said in an interview that the Obama administration has come to recognize that her industry and others faced the daunting prospect of competing against other sectors to install new pollution controls on a tight deadline.

“This is one of the most costly and complicated rules, and there’s going to be a lot of competition for these resources [to upgrade boilers and incinerators] all at the same time,” Harman said. “You can put a stricter and arbitrary deadline, but if it can’t be done, it can’t be done.”

Pew, the environmental lawyer, said that his group would challenge the new regulations in court but that “even if we win in court, it will be years till EPA gets around to doing this right.”

The Portland Cement Association welcomed the revisions. “EPA’s revised rule strikes the right balance in establishing compliance limits that, while still extremely challenging, are now realistic and achievable,” said Greg Scott, president of the industry group.

While formulating both the original and revised rules, the EPA came under pressure from a bipartisan coalition of lawmakers and governors to relax the standards, which were set in motion by the Clean Air Act amendments of 1990.

The House voted to repeal the previous boiler and cement rules, though the repeal failed to pass the Senate.

“Even though they are softer than earlier regulatory attempts on these, they should require pretty decent controls without big job losses,” said Frank O’Donnell, president of Clean Air Watch, an environmental advocacy group.

Heather Zichal, deputy assistant to the president for energy and climate change, met with industry officials opposed to the boiler rule and urged the EPA to forge a compromise, according to several individuals familiar with the meeting.

The EPA will also finalize a definition of solid waste along with the rules that would permit the burning of tires, railroad ties and plastic bottles, which boiler operators had sought so they were not regulated the same way as incinerators.

“They will be burning waste without controlling pollution,” Pew said.

Harman said that on average, two-thirds of the energy her members use for production comes from burning wood biomass. She added these facilities have to comply with federal air rules regulating other air pollutants beyond mercury and soot. “To say these emissions are just not being regulated is just not true.”

Both sides agree the rules have taken too long to complete: The cement regulations were supposed to take effect by 1997, and the boiler rules by 2000.

The Clinton administration proposed a cement rule in 1998, but it was thrown out in court for failing to regulate mercury and other toxic pollutants; a federal court threw out the 2004 boiler rule finalized under President George W. Bush on the grounds it should have imposed stricter rules on how boilers burned solid waste.

“EPA has said it is trying to find a middle ground on this regulation, advancing environmental and public health protections without unduly burdening industry and hindering the economic recovery,” said Richard Gold, who heads Holland & Knight’s public policy and regulation group and represents some of the manufacturers affected by the boiler rule.

“If the agency can strike that balance, it could be a first step toward a more collaborative relationship among EPA and its industry and environmental groups in Obama’s second term.”