The plaintiffs are the Native Village of Chickaloon, Natural Resources Defence Council, Center for Biological Diversity and Center for Water Advocacy.
They claim the National Marine Fisheries Service improperly issued exploration permits to Apache Alaska Corp. for high-intensity seismic exploration.
"Each year, there are fewer and fewer of these whales left," Taryn Kiekow, an NRDC attorney, said in an announcement of the lawsuit. "Oil and gas drilling activities expose Cook Inlet beluga whales to earsplitting underwater noise that threatens their survival. All that noise in the marine environment makes survival impossible for these endangered whales."
National Marine Fisheries Service spokeswoman Julie Speegle said from Juneau the agency would have no comment.
"Because it's a legal matter, we cannot comment," she said.
Beluga whales, which can reach 15 feet (4.5 metres) long, turn white as adults and feed on salmon, smaller fish, crab, shrimp, squid and clams. In late summer, belugas often can be spotted from highways leading from Anchorage, chasing salmon schooled at stream mouths.
From the 1980s on, the Cook Inlet population declined steadily from a high of about 1,300, and the loss was accelerated between 1994 and 1998 when Alaska Natives harvested nearly half of the remaining 650 whales. Belugas have not bounced back despite a hunting ban. A survey in June counted just 284 whales.
The federal government declared Cook Inlet belugas endangered in 2008. The state of Alaska fought the decision and said the listing would hurt economic development at the Port of Anchorage, the largest port in the state, as well as oil and natural gas development off the Kenai Peninsula.
The endangered species listing in November was affirmed by a federal judge, who rejected the state arguments that belugas already are protected by other environmental laws and that the fisheries service failed to consider state conservation programs designed to improve the habitat and food supply of belugas.
The lawsuit says Apache intends to explore for offshore oil and gas for 160 days a year using airguns that produce some of the loudest underwater sounds short of dynamite.
The lawsuit claims the noise is known to compromise foraging and other vital behaviour of whales, and that it can affect species over great distances.
The noise will be on top of already high levels of noise from industrial traffic and pollution, according to the lawsuit.
The groups claim the U.S. Marine Mammal Commission recommended against authorization for exploration, and that NMFS violated federal environmental law with its finding that seismic surveys would cause no significant impact.