The Natural Resources Defense Council (NRDC) and other environmental groups had successfully sued the navy in federal courts earlier this year on grounds of possible damage and injury to the region's dolphins, whales and sea lions, along with more than 30 other species of marine mammals in the area.
However, George Bush, the US president, intervened in the dispute by citing the necessity to US national security of the exercises and exempting the Navy from the environmental laws at the heart of the legal challenge.
The navy also argued the area off southern California is the only location on the
west coast that is relatively close to land, air and sea bases as well as amphibious landing areas.
A US appeals court later rejected the Bush administration's attempt to exempt the navy from the laws, prompting the administration to appeal to the Supreme Court and argue that the judges should have deferred to the judgment of the navy and Bush.
The ruling did not deal directly with the issue of environmental damage and Joel Reynolds, the director of the NRDC's marine mammal protection programme, said the ruling was "narrow" and did not establish "a bright-line rule".
"The court acknowledged that environmental interests are important, but in this case that the interest in training was greater ... than interest in the
environment," he told AP.