Trump administration officials earlier this year killed a federal criminal investigation into the coal empire owned by Sen. Jim Justice, a Republican from West Virginia and a close ally of the president’s.

The investigation examined potential criminal violations of the Clean Water Act by the multistate mining operations largely run by Justice’s son, Jay, according to current and former officials familiar with the matter.

The criminal probe was a significant escalation in the yearslong effort to police serial pollution offenses by Virginia-based Southern Coal and dozens of affiliated mining operations controlled by the family. In the past decade, Southern Coal and other Justice corporations have racked up tens of thousands of alleged violations of the Clean Water Act and have been sued repeatedly by state and federal prosecutors over their failure to properly follow environmental laws at their mining sites.

The investigation shuttered by the Trump administration was a joint effort by prosecutors and investigators with the Environmental Protection Agency, the Department of Justice’s Environmental Crimes Section and the U.S. Attorney’s Office of the Western District of Virginia to probe whether the incessant violations of antipollution laws had risen to the level of criminal behavior, people familiar with the matter said.

People familiar with the investigation told ProPublica that prosecutors believed they had a strong case. They initially had the blessing of Robert Tracci, President Donald Trump’s top official in the Western District of Virginia, to move forward.

But in recent months, as prosecutors battled the Justice companies in court over subpoenas for records, the Office of the Deputy Attorney General shut down the probe. At the time, Todd Blanche still headed the office, before assuming the role of acting attorney general in April.

“They were told ‘pencils down,’” a person familiar with the investigation said.

That prosecutors were even conducting a criminal investigation is noteworthy, people said, because the DOJ only charges a dozen or so criminal Clean Water Act cases each year. It is rare for top DOJ officials to derail a criminal investigation initiated by career officials at such an early stage, people familiar with the case said.

“I’ve never heard of that happening before,” said former federal prosecutor Rick Mountcastle, speaking generally about DOJ protocols. Mountcastle spent 24 years as a prosecutor in the Western District of Virginia. “There shouldn’t be some sort of untouchables list of people who are immune from enforcement.”

The move is part of a pattern of behavior at the top echelons of the DOJ to push cases against Trump’s political adversaries and ease up on allies.

Environmental enforcement against large polluters has plunged under the second Trump administration. Just days after inauguration, the administration reassigned top career environmental lawyers at the DOJ, including those overseeing the Southern Coal case, to work on the president’s immigration crackdown. At the beginning of the year, Blanche personally ordered prosecutors to stand down from cases against diesel emissions cheating.

Steven Ruby, an attorney for the Justice companies, said they became aware of the criminal investigation earlier this year.

“Ultimately the finding of the inquiry by the government was that there wasn’t any evidence to pursue criminal charges,” Ruby said. “There’s never been any intentional wrongdoing by the companies.”

While objecting to the subpoenas in court, the company simultaneously convinced the DOJ to drop the case, he said.

“The Justice companies — because Sen. Justice has been governor and because he’s now a senator — are singled out and put under a microscope, and there’s news coverage of violations and consent decrees and compliance actions,” Ruby said. “But the fact of the matter is that those kinds of issues exist throughout the industry.”

Current and former government officials familiar with the companies’ environmental record called them routine bad actors. 

Spokespeople for the EPA and the Western District of Virginia referred questions to the DOJ. Justice’s senate office did not respond to questions.

“There is no case to be made here for a criminal investigation,” Emily Covington, a DOJ spokeswoman, said in an email. “Any career prosecutor who would paint a criminal case as strong is simply a deep state prosecutor continuing to push the priorities of the Biden administration.”

The deputy attorney general’s office is routinely involved with reviewing cases, she added. The office determined that this case was not consistent with the Trump administration’s priorities, she continued, and it was more appropriate to resolve it through the less punitive civil process. “The bottom line is that this was a politically motivated prosecution for a case that can and should be resolved civilly,” she wrote.

The Justice family runs a sprawling coal mining enterprise that extends across the South. Estimates of its fortune fluctuate. Forbes tallied Jim Justice’s net worth to be as much as $1.9 billion until 2021; more recently, it declared him “broke” and facing $1 billion in debt. But environmental groups have accused his companies of misrepresenting their assets to avoid paying environmental penalties. 

Ruby said company finances seesaw because coal is a “boom and bust” industry.

Justice, who was first elected governor of West Virginia as a Democrat, announced he had become a Republican at a Trump rally in 2017. Trump backed Justice’s bid for Senate in 2023, amid a contested GOP primary. Justice went on to win the seat, helping Trump clinch a GOP majority in the Senate.

Coal mines often leach dangerous chemicals like arsenic into waterways and are required to strictly monitor pollution discharge and keep it under certain limits. The family’s companies have settled many accusations of environmental violations by agreeing to pay fines and invest in better pollution prevention without admitting or denying culpability.

In recent years, however, the company has repeatedly flouted regulators and the legal process. Jay Justice has been a no-show at court hearings involving Clean Water Act violations in the past, and in 2024 a judge in Alabama issued a civil contempt order against him for his repeated failure to respond to those lawsuits. Ruby, the Justice companies’ lawyer, attributed the violations in that case to surrounding facilities the family does not own. The case is now in mediation. 

A number of recent legal proceedings have laid bare the extent to which the Justice companies may have knowingly violated environmental laws, a key threshold for bringing a criminal matter. 

Such allegations surfaced in a 2023 civil case brought by the Justice companies’ former chief of environmental compliance Robert Fowler. In the suit, Fowler claimed that Jay Justice blocked him from spending the money necessary to comply with environmental laws, including making court-ordered payments and repairing equipment. As a result, according to emails disclosed in the lawsuit there were at times complaints of near-daily violations of permit water requirements.

In a resignation letter and in subsequent court filings, Fowler said he was concerned the circumstances exposed him to “potential civil and criminal liability.” Fowler declined to comment. 

The Justice companies denied Fowler’s accusations. The Justice companies believe the government’s criminal investigation was based primarily on Fowler’s claims, which Ruby dismissed as the allegations of a “disgruntled” former employee. 

Last month, a jury in Alabama found that the Justice companies had made false representations to Fowler about his role, but it did not award him the millions of dollars in damages he demanded in his lawsuit. The judge has yet to enter his final ruling.

In the DOJ’s aborted investigation of Southern Coal, prosecutors and federal agents had begun to gather evidence, scrutinizing testimony in the Justices’ various civil trials, and had approached former employees seeking information. Government attorneys also sent subpoenas seeking further documentation, said those familiar with the probe, a move that was opposed by the company’s lawyers.

People familiar with the case said Justice Department attorneys were ready to fight the Justices’ lawyers over the subpoenas.

But before they could move forward, Blanche’s office shut it down.