(CNN) Within hours of meeting with a mining company CEO, the new head of the US Environmental Protection Agency directed his staff to withdraw a plan to protect the watershed of Bristol Bay, Alaska, one of the most valuable wild salmon fisheries on Earth, according to interviews and government emails obtained by CNN.

The meeting between EPA Administrator Scott Pruitt and Tom Collier, CEO of Pebble Limited Partnership, took place on May 1, Collier and his staff confirmed in an interview with CNN. At 10:36 a.m. that same day, the EPA's acting general counsel, Kevin Minoli, sent an email to agency staff saying the administrator had "directed" the agency to withdraw an Obama-era proposal to protect the ecologically valuable wetland in southwest Alaska from certain mining activities.

In 2014, after three years of peer-reviewed study, the Obama administration's EPA invoked a rarely used provision of the Clean Water Act to try to protect Bristol Bay after finding that a mine "would result in complete loss of fish habitat due to elimination, dewatering, and fragmentation of streams, wetlands, and other aquatic resources" in some areas of the bay.

"All of these losses would be irreversible," the agency said.

The area is regarded as one of the world's most important salmon fisheries, producing nearly half of the world's annual sockeye salmon catch. Its ecological resources also support 4,000-year-old indigenous cultures, as well as about 14,000 full- and part-time jobs, according to the EPA's 2014 report.

Pruitt's move to rescind the plan to protect the area, if finalized, would allow Pebble to submit plans to mine there, but does not guarantee that those plans would be approved.

"This is a process issue," Collier told CNN in an interview. "[Pruitt] is not saying he's not going to veto this project. He's just saying that the rule of law says that you do an environmental impact statement first, right? That's Mr. Pruitt's position. And this is process, period. That's what we've always said."

Collier's spokesman, Mike Heatwole, told CNN three additional people were present at the meeting on May 1.

The EPA declined CNN's repeated requests for an interview with Pruitt, saying, most recently on September 5, that "we're focused on Hurricane Harvey and Hurricane Irma."

"The meeting was an opportunity for Administrator Pruitt to let [Pebble Limited Partnership] know that they are simply being granted a fair opportunity to apply; he did not prejudge the outcome of the process, nor make any assurances about the final decision on the project," Liz Bowman, an EPA spokeswoman, said in a statement issued to CNN on Friday.

The agency took issue with the fact that the EPA under the Obama administration moved to veto mining in Bristol Bay before permit applications had been filed.

"EPA's review will be based on the whole record, all the science and an actual proposal from the company," Bowman said.

Pebble plans to file mining permit applications in December, according to Collier.

'Homework assignment'

The communications with the new administration started well before the Pruitt-Collier meeting.

Pebble had been trying to get this administration's ear before Pruitt was even confirmed as President Donald Trump's pick to head the EPA, according to government emails obtained by CNN from a public records request under the US Freedom of Information Act.

On February 15, two days before Pruitt's swearing in, a lobbyist for the Pebble Partnership contacted a member of Trump's EPA transition team, according to the emails.

Bristol Bay's fisheries support about 14,000 full- and part-time jobs, according to a 2014 EPA report.

"As you may know, Pebble is trying to develop a world-class copper mine in southwestern Alaska," the lobbyist, Peter Robertson wrote. "We have yet to submit the first of the permit applications necessary to move ahead with the mine -- the permit application under section 404 of the Clean Water Act ... Do you have time for me to meet with you in the near future?"

The EPA transition staffer, David Schnare, replied the next morning.

"I am aware of the problem in general but do not have specifics," Schnare wrote. "Can you bring with you a timeline of events and a status on the legal actions? The preemptive strike by the last administration was indeed unprecedented and I don't want to see it become a precedent, particularly because it is a violation of Pebble's due process rights."

"In any case, I need to get this set up for the Administrator, which means I need the full background and a specific proposal on what we can and should do," Schnare continued.

"Without meaning to be flip, that's your homework assignment."

Schnare declined CNN requests for comment.

The emails between Robertson and Schnare were first obtained by the Natural Resources Defense Council, an environmental group, and were reported by E&E News.

"We requested that [Pruitt] would set this aside," Collier, the Pebble CEO, told CNN. "And the moment the election occurred he and his staff took a look and determined to do so."

"This was not a heavy lift," he said. "I mean this is something they ran on. You know, Scott Pruitt, you look at his statements for the last three years, every time he talks about environmental issues, the phrase he uses is 'rule of law.'

"And this was the classic rule of law case."

'Unlike anything I've ever seen'

Former EPA officials under the Obama administration expressed shock at how the decision was handled.

"That's incredible -- and very disappointing," Dennis McLerran, the former regional EPA administrator overseeing Bristol Bay and Alaska, said after reviewing some of the EPA's internal communications on the project. "The professionals, the career staff at EPA, the scientists put a tremendous amount of time and energy and effort into making sure that the decisions that we made were well grounded, that they were grounded in sound science."

McLerran called the revelations "stunning" and "unlike anything I've ever seen."

The EPA was being sued by Pebble for allegedly violating the Federal Advisory Committee Act by consulting with experts who opposed the mine without creating formal advisory committees to do so. A federal judge in November 2014 issued a preliminary injunction in that case, pausing the EPA's efforts to finalize a preemptive mining veto.

Given that legal process, it's "disturbing" and "extraordinary" that Pruitt would meet with Pebble's CEO under these circumstances, said Gina McCarthy, Pruitt's predecessor as head of the EPA. "It's very unusual when you're in litigation to unilaterally meet with the folks that are suing you," she said in an interview.

On May 11, Pruitt and Pebble settled the outstanding lawsuit.

"We are committed to due process and the rule of law, and regulations that are 'regular,'" Pruitt said in an EPA press release issued on May 12. "We understand how much the community cares about this issue, with passionate advocates on all sides. The agreement will not guarantee or prejudge a particular outcome, but will provide Pebble a fair process for their permit application and help steer EPA away from costly and time-consuming litigation."

'These losses would be irreversible'

It's unclear exactly what size mine the Pebble Partnership will propose.

Collier told CNN he will submit permit applications for a mine "footprint" that's about 5 square miles in area. The EPA's 2014 reviews of potential mine operations, however, found that the mine could be much larger, potentially the "largest open pit mine ever constructed in North America." In total, EPA's peer-reviewed analysis of Bristol Bay found, based on Pebble's SEC filings, the mine site could cover an area the size of Manhattan. And the pit could be about 80% as deep as the Grand Canyon.

Collier maintains the mine will be far smaller than the EPA suggested, and that it will be small enough that it would have passed the EPA's own review of what is environmentally acceptable.

"This is a project that doesn't present the kind of environmental boogeyman that a lot of the environmental community has been saying it does," Collier said.

"Where we're going to start with this project, our permit application that we'll file which will govern the first 20 years of construction, is going to be a project that is almost the size that the EPA, the Obama administration EPA, would have let us build here."

The legal battle is likely far from over, though.

The Natural Resources Defense Council, the environmental group, told CNN in a statement that if the EPA moves forward it "will fight the Pebble Mine" -- in court, if necessary.

The EPA is accepting public comments on its proposal through October 17.