WASHINGTON — Environmental Protection Agency Administrator Scott Pruitt announced late Friday that he will not scrap the agency’s 2014 determination that a large-scale mining operation could irreparably harm Alaska’s Bristol Bay watershed.

His decision, which falls short of blocking a proposed gold and copper mine in the region outright, represents a surprising twist in a battle that has pitted a Canadian-owned mining company against commercial fishing operators, native Alaskans and conservationists determined to protect the world’s largest sockeye salmon fishery.

Last spring, shortly after meeting with the top executive from the main company backing the project, Northern Dynasty Minerals, Pruitt directed EPA staff to revisit the Obama-era decision to short-circuit the project using a provision of the Clean Water Act.

The 2014 EPA decision came following several years of scientific study during which the EPA determined that the mining operation could cause “significant and irreversible harm” to the area’s fish habitat.

On Friday, after receiving more than 1 million public comments and consulting with tribal governments and others, the EPA said it will leave the previous administration’s determination in place while it takes further comments.

But the announcement said the decision “neither deters nor derails the application process” for the mine.

“It is my judgment at this time that any mining projects in the region likely pose a risk to the abundant natural resources that exist there,” Pruitt said in a statement. “Until we know the full extent of that risk, those natural resources and world-class fisheries deserve the utmost protection.”