That’s because the agency has long counted not just the direct health benefits of pulling a certain pollutant out of the atmosphere, but also what are called the “co-benefits” that occur when, as a result, other toxins are also reduced.

For example, in the case of the mercury rule, the Obama administration found between $4 million to $6 million in health benefits directly from curbing mercury. But it further justified the regulation by citing an additional $80 billion in health benefits a year by, among other things, preventing as many as 11,000 premature deaths. Those savings come from a reduction in particulate matter linked to heart and lung disease that also occurs when cutting mercury emissions.

Mr. Konkus, the E.P.A. spokesman, said last week, “One of a number of issues E.P.A. is assessing in the context of the appropriate and necessary analysis is whether and how to account for co-benefits.”

A powerful array of business groups including the United States Chamber of Commerce, the National Association of Home Builders and leaders in the coal industry say the E.P.A. has for too long ignored or downplayed in its formulas the costs of regulations to their businesses .

One of the fiercest critics is Robert E. Murray, the C.E.O. of Murray Energy Corp., who has donated to Mr. Trump’s inauguration fund, and has served as a chief counselor to the president on his efforts to revive the nation’s flagging coal industry. Mr. Murray helped underwrite lawsuits that Republican attorneys general and industry groups brought against the mercury rule. He cited its repeal as one of his top priorities in letters last year to cabinet heads.

Mr. Murray is also a former lobbying client of Mr. Wheeler , the current acting administrator of the E.P.A. who joined the agency after spending nearly a decade as the coal executive’s top attorney.

Mr. Konkus said that Mr. Wheeler did not work on the mercury issue when he served a lobbyist for Mr. Murray, and said Mr. Wheeler did not lobby the agency at all in the two years before joining in April. Mr. Wheeler signed a statement in which he recused himself from working with former clients, including Murray Energy, until April 2020.