ANCHORAGE — Royal Dutch Shell’s quest to drill exploratory wells in Arctic waters has received a boost with the affirmation that its federal air permits for the Chukchi Sea were properly granted.

The EPA Appeals Board on Thursday rejected challenges to the air permits brought by Alaska Native and conservation groups.

Shell Alaska spokesman Curtis Smith said in a formal announcement that the decision means Shell, for the first time, has usable air permits that will allow its drill ship, the Noble Discoverer, to work in the outer continental shelf off Alaska’s northwest coast in 2012.

“Achieving usable permits from the EPA is a very important step for Shell and one of the strongest indicators to date that we will be exploring our Beaufort and Chukchi leases in July,” Smith said.

Drilling is strongly opposed by conservation groups that contend oil companies cannot clean up a spill in ice-choked waters, and that the remote Chukchi and Beaufort seas are too far from ports, major airports and other infrastructure for an effective cleanup if there’s a blowout.

Earthjustice attorney Colin O’Brien, who represented groups that filed one of four air permit appeals, said in an email response to questions that the decision could be appealed in federal court, but that it was too early to speculate about potential next steps.

He said EPA took shortcuts when it issued the permits and failed to fully protect Arctic air quality as required by the Clean Air Act.

“These permits pave the way for Shell to emit thousands of tons of harmful air pollution into the pristine Arctic environment, at levels that may be harmful to nearby communities and the environment for years to come,” he said. “We are disappointed that the Environmental Appeals Board decided against us and allowed EPA’s permit decisions to stand.

A Shell subsidiary has applied to drill up to three exploratory wells in the Chukchi during the open water season this year and additional exploratory wells in 2013. The company hopes to use a second drill for exploratory wells in the Beaufort Sea off Alaska’s north coast, and awaits a decision on the appeal of its air permit.

The Bureau of Ocean Energy Management in December approved Shell’s Chukchi drilling plan with one important stipulation. The agency said Shell must stop drilling into hydrocarbon zones 38 days before sea ice is projected to engulf the drill site to make sure it has time cope with a spill or a wellhead blowout. That would cut the drilling window by about one-third.

A successful appeal of previous air permits played a part of Shell’s decision to cancel drilling for 2011. In that case, the appeals board concluded that analysis of the impact of nitrogen dioxide emissions on Alaska Native communities was too limited. The board remanded the permits to allow the agency to fix permit problems.

The appeal filed by Earthjustice contended that Shell’s new permit was based on pollution estimates that were inherently unreliable because they are based on equipment that Shell did not identify and that the EPA never intends to test.

Shell faces other hurdles before it can send its drill ships and support vessels north. The Bureau of Safety and Environmental Enforcement must approve Shell’s oil spill response plan for the Chukchi.