JUNEAU — The U.S. Environmental Protection Agency, while a lawsuit is pending, must stop all work related to a process that could restrict or prohibit development of the Pebble Mine, a federal judge says.

The action comes after U.S. District Judge H. Russel Holland last month restrained the EPA from taking any action toward a possible decision to veto a mine project until he ruled on the merits of a lawsuit brought by the group behind the mine, the Pebble Limited Partnership.

The partnership sued earlier this year over an EPA study that concluded large-scale mining posed significant risk to salmon in Alaska’s Bristol Bay region. The study provided the basis for the agency to invoke a rarely used process under the Clean Water Act that mine supporters fear could result in the project’s veto before it goes through the permitting process.

The EPA sought clarification last week on what Holland’s order encompassed.

Attorneys for the agency said barring the EPA from activities such as communicating with outside parties would “create substantial harms” for the agency. They said it would disrupt review of public comments and create confusion about whether the EPA can respond to public questions or communicate internally about the matter.

In an order dated Thursday, Holland said the EPA cannot engage in any activities related to the process until a ruling has been made.

He also laid out a filing schedule that calls for Pebble to submit an amended complaint by Dec. 19.