National security interests outweigh the possible harm to marine life, a three-judge panel of the 9th U.S. Circuit Court of Appeals determined in overturning a judge's order banning the practice.
"The public does indeed have a very considerable interest in preserving our natural environment and especially relatively scarce whales," Judge Andrew Kleinfeld wrote for the majority. "But it also has an interest in national defense. We are currently engaged in war, in two countries."
Judge Milan Smith Jr. disagreed, saying he would have kept the ban in place in part because the Natural Resources Defense Council is likely to win its lawsuit to stop the use of sonar.
The ruling allows the Navy to use the sonar in 11 planned training exercises.
Cara Horowitz, an attorney for the Santa Monica-based resources defense council, said she was "somewhat disappointed" by the ruling Friday, but remained confident the lawsuit would quickly succeed in shutting down the sonar program off the Southern California coast.
The appeals court said in its Friday ruling that it wanted to resolve the lawsuit quickly and Horowitz was hopeful that the Navy will be able to undertake most of the 11 planned exercises. She said the next planned exercise is in September.
The council's lawsuit alleges that the Navy's sonar causes whales to beach themselves among other environmental harms.
The Navy maintains it already minimizes risks to marine life. It has monitored the ocean off Southern California for the 40 years it has employed sonar without seeing any whale injuries.
A Department of Justice attorney didn't return a telephone call Friday.