JUNEAU — A federal judge is scheduled to hear arguments Thursday in a case alleging that the U.S. Environmental Protection Agency worked with critics of the proposed Pebble Mine with a predetermined goal to block the project.

The lawsuit was brought by the Pebble Limited Partnership, which is seeking to advance the project near the headwaters of a world-premier salmon fishery in Alaska. Pebble alleges that the EPA violated a federal law by establishing and working with groups of mine critics that essentially acted as advisory committees but failed to comply with requirements of that law, such as noticing meetings or making available transcripts.

But the EPA in court records says Pebble’s lawsuit fails to mention the “countless contacts” Pebble had with the EPA, and it sees the case as a bid to undermine the agency’s proposal to protect parts of the Bristol Bay region from development. It wants the case dismissed.

Arguments are scheduled for Thursday in Anchorage on whether the case should advance.

The project, which has not entered the permitting process and is seeking another partner to invest, has been the subject of a long-running public relations and legal battle

The EPA released a report last year concluding that large-scale mining in the Bristol Bay watershed posed significant risk to salmon and could adversely affect Alaska Natives in the region, whose culture is built around salmon. The agency later initiated a rarely used process through which it ultimately could restrict or prohibit development of the massive gold and copper prospect, which Pebble blasted as an overreach.

U.S. District Court Judge H. Russel Holland in December ordered the EPA to stop all work related to that process pending a ruling on the merits of the case.

Pebble spokesman Mike Heatwole said Wednesday that what Pebble wants is an opportunity to have the project “fairly and objectively analyzed” through the normal environmental review process, as other projects are.

Pebble, in court documents, says the EPA had long ago decided to block the project and reached the decision after “secretive consultations” with outside organizations and individuals critical of the project. Pebble attorneys point to a 2010 document that includes options for the EPA involvement surrounding Pebble. It was included in an email between two EPA employees that Pebble says was produced as part of a public records request.

“In short, by the time Plaintiff and other mine supporters were permitted to have their say, the fix was in, and nothing that Plaintiff could say or do would change the outcome,” Pebble attorneys said in court documents.

Attorneys for the EPA say the draft “options paper” presents possibilities for the EPA to consider in deciding whether and how to exercise its regulatory authority, not a predetermined outcome. Even if the document was shared with an attorney for mine critics — a point the government says it does not concede — it doesn’t show a violation of the Federal Advisory Committee Act because getting input from one individual is not a violation, government attorneys said in court documents.

In a statement Wednesday, the EPA said it spent three years evaluating science, conducting hearings and reviewing comments in developing its watershed assessment. “No process could have been more transparent and inclusive of all views, including for proponents of the Pebble Mine,” the agency said.