The court heard arguments in a dispute between the Bush administration and environmental advocates over court rulings that restrict sonar in naval training exercises off the coast of Southern California.
The administration says the training is vital for teaching sailors how to find enemy submarines.
"I see an admiral come along and say you have to train under these circumstances," Justice Stephen Breyer said. "I'm very nervous about it."
There is also evidence that the technology has caused whales to strand themselves on shore.
The exercises have continued since thethat the Navy must limit sonar use when ships get close to marine mammals.
Richard Kendall, representing the Natural Resources Defense Council, told the justices that the Navy is managing under the restrictions, noting that eight of 14 planned exercises have been completed since the restrictions took effect.
This round of training is scheduled to be complete by January.
Separately, the Navy has agreed to similar limits on anti-submarine training off the coast of Hawaii to settle a lawsuit.
But Solicitor General Gregory Garre said the issue for the court is whether federal judges should have stepped in to force changes to the training when the government's first environmental assessment found there was little prospect of harm to whales and dolphins.
The Navy's own environmental assessment of using sonar during the 14 training exercises off the California coast found that it could disturb or harm an estimated 170,000 marine mammals, including possible temporary hearing loss in at least 8,000 whales.
But only five whales have been stranded and 37 whales have died because of sonar since 1996, the Navy says.
In addition, Garre said, the Navy has used mid-frequency sonar in training exercises off Southern California's coast for 40 years.
The Bush administration also says the president has the power to override federal court rulings on environmental laws during emergencies that include harm to national security. The Navy says it has already taken steps to protect beaked whales, dolphins and other creatures and is balancing war training and environmental protections.
Justice David Souter ridiculed the idea that the administration could declare an emergency to try to get around complying with environmental laws. The Navy opted not to conduct a more rigorous environmental study before beginning the long-planned exercises, Souter said.
"If there's an emergency, it's one the Navy created simply by failing to start EIS preparation in a timely way," he said.
Justice Samuel Alito suggested that he found little evidence in the court record that the marine mammals would be harmed by the sonar use.
Alito also said there was "something incredibly odd" that a single federal judge, who issued the first order against the Navy in this case, would be able to force changes in the exercises.
An injunction by U.S. District Judge Florence-Marie Cooper in Los Angeles early this year created a 12-nautical-mile no-sonar zone along the coast and ordered the Navy to shut off all sonar use within 2,200 yards of a marine mammal.
The 9th Circuit sided with the lower court and said the Navy must abide by the injunction. However, while the litigation was under way, the appeals court gave the Navy permission to use sonar closer than the restrictions allow during critical maneuvers.
The case is Winter v. Natural Resources Defense Council, 07-1239.