A coal and gas extraction firm, Hallador Energy said it got the low-interest loan from the Paycheck Protection Program, a nearly $350 billion fund designed to bolster small businesses during the downturn. The program quickly ran out of money in the face of wide-scale demand: Congress and the White House are nearing a deal that would provide about $310 billion to replenish the fund.

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The program was designed for companies with fewer than 500 workers but has been tapped by firms that are far larger.

The administration is now facing a backlash for giving millions of dollars to national hotel and restaurant chains before the program ran dry. One of them, the burger chain Shake Shack, decided to return the $10 million loan it got from the program.

Under Small Business Administration guidelines, some bituminous-coal-mining firms with up to 1,500 employees can qualify for the loans. The Terre Haute, Ind.-based Hallador had a head count of 768 as of March 9, according to a filing with the Securities and Exchange Commission.

Asked about the loan, agency spokeswoman Carol Wilkerson said in an email Tuesday, “Under SBA’s Small Business Size Standards, mining operations allows for more than 500 employees.”

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The program aims to keep workers employed by extending loans that are forgivable if their employers keep workers on the payroll. Hallador said in a statement that it plans to use its loan to pay employee salaries for two months, along with other expenses. The company did not reply to questions about the loan.

With unemployment levels not seen since the Great Depression, the lending program has been overwhelmed and has left thousands of traditional small businesses without aid. Hallador’s SEC filing saying it had been approved for the loan came Wednesday, a day before the SBA announced that the program had run out of money and that it was no longer accepting new claims.

Several Democrats and environmental groups have called for barring any coronavirus-related money from going to oil, gas and coal firms, arguing they are helping fuel climate change. “No bailouts for the fossil fuel industry,” tweeted Sen. Edward J. Markey (D-Mass.).

Like many other U.S. coal-mining companies, Hallador and its main subsidiary, Sunrise Coal, has shrunk as coal-fired electricity generation in Indiana fell by 30 percent over the past decade because of stiff competition from cheaper gas and wind sources.

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Pruitt was brought in to help mount an ultimately unsuccessful effort by Hallador to persuade Indiana state legislators to stop two of the state’s electric utilities from moving forward with plans to close most of their coal plants.

President Trump often touts the benefits of “beautiful, clean coal,” and during Pruitt’s 17-month tenure heading the EPA, the administrator cast the Obama administration’s efforts to fight climate change as a “war against coal.” He also started unraveling rules designed to reduce pollution from the mining and burning of coal.

But Pruitt was unable to see through many of those rollbacks after resigning as EPA head in 2018 under a cloud of ethical and managerial lapses.

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When it hired Pruitt as a lobbyist, Hallador ran four coal mines in southwestern Indiana. But in February, the firm decided to shut down one of them. It began the year with 915 full-time employees and temporary miners but reduced its head count to under 800 by early March.

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With a market valuation of about $21 million, though, Hallador is still not most people’s idea of a small business.

In 2018, it dug up 7.6 million tons of coal, making it the country’s 18th-biggest producer by weight that year, according to Energy Information Administration data. The firm, whose motto is “Coal Keeps Your Lights On,” also has a stake in an Indiana gas exploration company and in an operation that mines sand in Colorado for use in hydraulic fracturing.

The entire U.S. coal sector has suffered from competition from cheaper natural gas and renewable energy sources and, more recently, a decline in electricity demand because of the pandemic. And the Illinois Basin, where Hallador mines its coal, “is probably at the moment the hardest-hit basin” in the country, according to Chiza Vitta, an analyst with S&P Global Ratings.

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Locked in the interior of the country, the coal-mining region stretching through Illinois, southwestern Indiana and western Kentucky lacks good port access to overseas markets. And unlike Appalachia, it also has little high-quality coal suitable for steel production. One of the region’s leading producers, Foresight Energy, filed for bankruptcy protection last month.

In addition to Pruitt, there is at least one other connection between the Trump administration and Hallador. Suzanne Jaworowski, Hallador’s former communications and government affairs director, now works as a senior adviser at the Energy Department’s Office of Nuclear Energy. She was also the state campaign director in Indiana for Trump’s 2016 presidential run.

Jayson O’Neill, executive director of the liberal advocacy group Western Values Project, said in an email that Hallador’s loan reveals a flaw in the administration’s approach to addressing the outbreak’s devastating economic impact.