The Environmental Protection Agency is coming under increased scrutiny over accusations that it rigged its own review process to block the Pebble Mine project in Alaska.

The House Science, Space and Technology Committee is scheduled to weigh in Thursday with a hearing on whether EPA officials orchestrated an environmental assessment in concert with anti-mine groups to reach a predetermined outcome.

Exhibit A is an explosive Oct. 6 report by the Cohen Group, headed by former Defense Secretary William Cohen, which cited the EPA’s “unprecedented” evaluation process, including its decision to use procedures under the Clean Water Act instead of the National Environmental Policy Act to assess the project.

The 346-page report, commissioned by the Pebble Limited Partnership, the project’s developer, also said that the statements and actions of EPA officials raised “serious concerns” about the agency’s objectivity and transparency.

“This project is too important, for all stakeholders, to pilot a new, untested decision-making process,” said Mr. Cohen in the report. “The fairest approach is to use the well-established Permit/NEPA Process, and I can find no valid reason why that process was not used.”

Rep. Lamar Smith, Texas Republican and committee chairman, said this week that the agency’s behavior on the Pebble Mine project “demonstrates how the EPA is truly out of control.”

“Secretary Cohen’s report lays out evidence that shows collusion and a cozy relationship between the EPA and groups actively opposed to the Pebble Mine,” said Mr. Smith. “These relationships could inappropriately influence EPA’s ability to conduct policy based on sound science.”

In a statement Tuesday, the EPA defended its July 2014 proposed restrictions on the Pebble Mine, saying that the vast size of the project and its overlap with sockeye salmon fisheries in Bristol Bay justified the use of the agency’s authority under the Clean Water Act’s Section 404(c).

“EPA use of its authority has typically involved major projects with significant impacts on some of America’s most ecologically valuable waters,” said the statement. “EPA Region 10’s proposal to protect the Bristol Bay watershed outlines restrictions that would protect waters that support salmon in and near the Pebble deposit. These restrictions apply to impacts associated with large-scale mining of the Pebble deposit. No other lands or development are subject to the restrictions.”

Taryn Kiekow Heimer, senior policy analyst at the Natural Resources Defense Council, said the EPA’s July 2014 proposal limiting mining activity at the Bristol Bay watershed was needed to protect salmon from “the potentially catastrophic effects of large-scale mining.”

As for accusations of agency bias against the Pebble Mine, she blasted the Cohen report for what she called its “lack of independence, credibility, and transparency,” saying that it echoed “the same arguments that the Pebble Limited Partnership and its bevy of other paid consultants have made for years.”

“It adds nothing new to the dialogue,” said Ms. Heimer in an email. “Thursday’s hearing will just rehash a biased and flawed report and won’t add anything new to the dialogue.”

The Pebble Mine project, touted for more than a decade, targets a vast deposit of porphyry copper, gold and molybdenum on state land in a remote region of southwest Alaska with an estimated value of $400 billion.

Mr. Cohen, who authored the report with DLA Piper LLP, was known during his tenure in the Senate as a moderate Republican — he represented Maine and served as Defense Secretary under President Clinton, a Democrat.

In the report, he notes that the developers had not submitted a permit application, and therefore the EPA’s assessment was based on “hypothetical scenarios rather than the characteristics of a mine as it was actually planned to be built and maintained.”

The process also inhibited the involvement of Alaska officials and failed to take into account “mitigation and control techniques a developer might propose.”

Records obtained through Freedom of Information Act requests found hundreds of meetings and communications starting in 2009 between opponents of the project, including members of Trout Unlimited and an attorney for tribes and environmental groups.

“The substance of these contacts progressed from expressions of a point of view and interest in participating in the evaluation of a Pebble mine to substantive advice on legal and policy strategies and scientific information in support of the BBWA [Bristol Bay watershed assessment] and a Section 404(c) action,” said the report.

Thursday’s House committee hearing features Mr. Cohen and Pebble Partnership CEO Tim Collier, but the committee plans to have the EPA testify at another hearing in the coming weeks, according to staff.

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