This story was updated at 6:18pm on 1/17/2014.

The Environmental Protection Agency’s (EPA) report from Wednesday, on Alaska’s giant proposed Pebble copper mine, may reveal government leanings on a potential controversial project veto, according to a lawyer party to the dispute.

The secret lies in Appendix J of the report, which runs to well over 1000 pages in three volumes, according to Anchorage attorney Geoffrey Parker. He has represented Alaskan native tribes in their fight to defeat the project.

That section deals with how mine developers, like Northern Dynasty Minerals Ltd. (TSX:NDM), can mitigate expected environmental damage. But the appendix represents one of the few major changes in the report from its previous April 2013 version, Parker said.

Parker suggests that the revision indicates that the EPA can, and should, veto the Pebble mine under the Clean Water Act, which allows them to veto projects harmful to wetlands.

That appendix “is on compensatory mitigation of unavoidable impacts, and unavoidable impacts are an excellent basis for using 404C,” he told IBTimes. “It’s the only part of the assessment that I’ve spotted that almost doubled in length. Everything else remained really similar.”

The release of the final report was viewed as a milestone in a years-long controversy, and an indication of the EPA’s views on the project, which has been in the works for years. The agency has stressed that it doesn’t yet have an official stance on the Pebble project, and that its report is meant to be an objective scientific assessment with no policy implications.  

The EPA declined to comment on the appendix. “EPA has been focused on finding the best, most current science on the Bristol Bay watershed,” wrote an EPA spokeswoman to IBTimes. “We will be evaluating options.”

Suggestions by industry and the public for minimizing the mine’s impact on nearby water systems don’t seem realistic or sustainable, on a close reading of the appendix.

“There are significant challenges regarding the potential efficacy, applicability and sustainability of compensation measures proposed by commenters for use in the Bristol Bay region, raising questions as to whether sufficient compensation measures exist that could address impacts of the type and magnitude described in the Bristol Bay Assessment,” reads the appendix’s revised conclusion, which is significantly beefed up from its April 2013 version.

In plain English: it’s tough to blunt the mine’s expected environmental impacts in a way consistent with regulations.

Peer review experts who vetted the government report found revisions to the 38-page appendix important.

“Appendix J (to my reading) strongly indicates that compensatory mitigation is essentially inapplicable to the Bristol Bay watershed,” wrote University of Idaho adjunct professor Charles Slaughter in his review of the final report.

“Revise to perhaps something more along the lines of “No viable alternatives could be identified to address impacts of this type and magnitude,” added peer reviewer Dennis Dauble, of Washington State University.

The appendix’s lead author and EPA employee Palmer Hough didn’t return a request for comment.

“Regulations recognize that there may be instances when the ACOE [U.S. Army Corps of Engineers] cannot issue a permit ‘because of the lack of appropriate and practicable compensatory mitigation options,” reads the appendix.

Developers have pointed out that the U.S. Army Corps of Engineers usually handles the relevant type of permits, and have argued that the EPA shouldn’t interfere by pre-emptively vetoing the project. Developers haven’t yet filed permits, though they’ve submitted detailed mine plans to the Securities and Exchange Commission.

The EPA hasn’t yet taken an official stance on a veto, either. The use of Clean Water Act vetos could have wider ramifications on U.S. mine development, points out a recent Wall Street Journal editorial, by chilling development and killing jobs.

“Using the report to reach decisions on the Pebble project - as project opponents urge the EPA to do - would contravene the very NEPA [National Environmental Policy Act permit] process environmental groups insist is the only measure to properly evaluate a mine," wrote consultant Daniel McGroarty to IBTimes, speaking for the American Resources Policy Network.

The appendix language does imply that any large mine project in the wider Bristol Bay region, and not just the proposed Pebble mine, would fail to mitigate its damaging footprint, according to Parker. Ten specific claims for other copper deposits have been filed in the Nushagak and Kvichak River watersheds, according to the EPA’s executive summary.

Still, even environmental lawyers opposed to Pebble caution against reading too much into the report.

“Dennis McLerran (and others at EPA) have gone out of their way not to burden this watershed assessment with statements about regulatory intention,” wrote Natural resources Defense Council attorney Joel Reynolds to IBTimes.

“It is possible to read various statements in or about the assessment as suggesting what EPA will do next -- and I think the law and facts clearly dictate that they proceed with 404c [veto] action -- but what they will actually do remains a guessing game,” he said.

Northern Dynasty CEO Ron Thiessen laid out several mitigation measures to IBTimes in a November interview, arguing that it a “physical impossibility” for the mine to impact 80 percent of nearby fish, because salmon spawning habitats aren’t located in the two most affected watersheds.

He cited mines near Canada’s Fraser river watershed as having manageable environmental impacts and as being similar to Pebble’s plan.

“What you’re hearing from these e-NGOs [environmental NGOs) is Orson Welles’ War of the Worlds,” Thiessen told IBTimes.  “Common from their blather is that they’re both well-conceived and well narrated fiction.” He is confident that the proposal will stand up to environmental regulatory scrutiny, if reviewed by the U.S. Army Corps of Engineers.

Update: John Shively of the Pebble Partnership emailed IBTimes and added: "We disagree with the conclusion that mitigation measures will not work.  There are numerous instances of fish habitat mitigation measures working around the world and in Alaska...In addition, EPA never puts the impacted areas into any context. Although they suggest dozens of miles of streams and rivers could be affected, EPA neglects to let people know that there are thousands and thousands of miles of rivers and streams in the Bristol Bay watershed. Similarly, they neglect to show the relationship of the number of acres of wetlands that might be impacted and the number of acres of wetlands in the 40,000 square mile area that is the Bristol Bay watershed."