The groups say NMFS improperly granted the permit to Apache Alaska Corp. for seismic exploration that will include earsplitting underwater noise that threatens the survival of the whales.
The plaintiffs are the Native Village of Chickaloon, the Natural Resources Defense Council, the Center for Biological Diversity and the Center for Water Advocacy.
A survey last June counted 284 whales, down from a population of about 1,300.
NMFS spokeswoman Julie Speegle says the agency can't comment on pending litigation.
