A new study examining efforts by Pebble mine developers to reclaim land disturbed by years of exploration work finds deficiencies by both the operator and the state agency that oversees mining.

Plans for a massive gold and copper mine at the headwaters of Bristol Bay are stalled while Pebble Ltd. Partnership, the developer, searches for new investors and battles the U.S. Environmental Protection Agency in federal court.

Pebble says its site is heavily monitored by state agencies and complaints of environmental harm have repeatedly been found baseless.

Exploratory drilling done from 2004 to 2012 left its own mark, and Alaska Native organizations along with remote lodges last year petitioned the state Department of Natural Resources to ensure proper restoration work is done, given Pebble's finances.

The study released Thursday was commissioned by the United Tribes of Bristol Bay, which represents 14 tribal governments, and was conducted by the Center for Science in Public Participation. The latter, based in Bozeman, Montana, provides technical help to tribes and grass-roots groups on mining projects. Pebble says the study authors have spoken out against Pebble and are not independent. The researchers defend their work as objective science.

A Center for Science team that included a geochemist, geophysicist and a tribal member from Nondalton flew by helicopter this summer to spend five days on the Pebble mine site examining drilling holes and waste sites. A state DNR team separately spent two days inspecting sites.

Pebble has reported drilling 1,355 holes in the tundra as it evaluated its prospect. DNR said the mine developer is following the rules and plugging holes except for ones it still intends to use. But both DNR and Pebble have found some plugs are not holding in place.

The science center study focused on drill holes with water issues, as well as older and deeper borings, the authors said. The sample wasn't necessarily representative though the team also checked a number of sites with no previous concerns.

The CSPP group, which inspected 100 boreholes and seven other sites, found several areas of trouble beyond what DNR or Pebble noted.

Some holes weren't plugged at all, its report said. Drill cuttings left atop the ground in some spots were leaching acid. Even when waste was buried, tundra mats or other vegetation placed on top had died from apparent lack of care. Groundwater seeping up from holes brought with it heavy metals, including potentially toxic levels of copper.

And numerous steel pipes used to stabilize boreholes were sticking up from the ground, posing a risk for snowmachine travel, the CSPP study found.

In all 71 of the 107 inspected sites "were not fully reclaimed," based on observations of dead vegetation, flowing water and open and abandoned drill casings, its report said.

"There is some environmental degradation out there. It is not terrible," said David Chambers, report co-author and founder and president of the Center for Science. "But the major point is that there is work out there that needs to be done and because of the remote location out there, it is going to be very expensive to do it."

DNR needs to do more inspections itself, said Chambers, a geophysicist. It also should stop Pebble from leaving drill cuttings in the open because of its newfound evidence of acidic soils from waste material exposed to the elements, the center said.

The mine project is highly contentious because it would impact streams essential to Bristol Bay's world-class wild sockeye salmon runs. The tribal group is among many organizations in the region fighting the gold, copper, silver and molybdenum mine, though some Native-run corporations that have benefited from Pebble contracts have urged an open mind.

Industry experts have not found evidence of acidic soils, or other degradation, Pebble said.

The evidence of acid is new from this summer's testing, said Chambers, the study co-author. He hopes to publish the findings in a professional journal.

The last state inspection, completed this summer over two days, "found Pebble to be in full compliance with its permits," Pebble spokesperson Mike Heatwole said in an email. "Pebble receives more intensive regulatory oversight and scrutiny than any other mineral exploration site in the state, with more than 55 inspections since 2003."

The new study doesn't include enough data or information about its methods, including whether outliers were excluded, the mine developer said. And some of what is called contamination may just be the result of the natural mineralized state of the deposit, Pebble said. The researchers may have mistaken existing rock for cuttings, the developer said. But Chambers said the material studied was from drilling.

DNR agreed that Pebble is complying with permits and state standards — and said it is stepping up its own role. Pebble responds when issues come up, DNR said.

"The operator identifies and addresses maintenance and repair issues on site and is consistent to industry best management practices," the agency reported after its July site inspection.

DNR says it has looked at hundreds of Pebble bore holes, including all those with issues, up to now. Just this year the agency said it inspected 141. Six DNR employees contribute to oversight of Pebble, plus staff members at the state departments of Environmental Conservation and Fish and Game.

This year, DNR inspected drill holes with known issues and, for the first time, a random sampling as well, said agency spokesperson Elizabeth Bluemink. Before, DNR targeted spots where it had questions or that had issues, such as "artesian flows," essentially water in the ground moving up drill holes and onto the surface.

Random sampling helps to determine the overall condition of the state land leased by Pebble, and will continue, DNR said.

"We are now doing both types of site visits — focused and random — in our inspections," Bluemink said in an email.

But those aren't always thorough inspections, said United Tribes of Bristol Bay. Some are checked by flying over.

"They haven't even looked at the vast majority of the holes," said the Dillingham-based group's executive director, Alannah Hurley.

A particular concern are pipes, typically steel, inserted into the ground to give stability to drill holes. Some have been cut off to ground level, the normal practice for closing in a drill hole along with filling or capping. But many stick up from the ground, a steel hazard for snowmachiners, she said.

People who cross the land on snowmachine generally know about the mine work, Heatwole said. Some structures remain and some drill holes are being kept open for future work and monitoring, he said. They are marked with highly visible stakes, he said. DNR said that it asked Pebble to flag any protruding steel pipes.

"We are working to make sure the rest are covered," Heatwole said. "Holes that are officially closed are cut to ground level and grounded."

As to dead vegetation, it will be replaced once the soils stabilize, he said.

Pebble has just applied for permission to continue reclamation, monitoring and storage through 2018. Its current permit for "care and maintenance" expires at year's end. The state issued what it called a courtesy public notice about the application this week.

DNR was sued earlier for failing to provide public notice for more intensive exploration work by Pebble. The Supreme Court ruled last year that it must provide notice for that type of work.