The Navy says the $300 million system, intended to sweep 80 percent of the world's oceans, is important to national security because other nations such as Russia, Germany and China are developing super-quiet submarines to avoid traditional detection.
The Commerce Department's National Marine Fisheries Service granted the Navy a five-year exemption from the Marine Mammal Protection Act, allowing what opponents maintain will be "harassment" of marine mammals with the intense low-frequency sonar.
The Navy, which plans to use the new sonar on two warships, will be required to visually monitor for marine mammals and sea turtles and to turn off the sonar whenever any such creatures are detected in the area. The original plans called for four ships but were scaled back due to budget constraints.
"Marine mammals are unlikely to be injured by the sonar activities and ... the sonar will have no more than a negligible impact on marine mammal species and stocks," agency officials said in a statement Monday.
The exemption for the Surveillance Towed Array Sensor System, or Surtass LFA, is due to be reviewed on an annual basis.
Whales are particularly susceptible to sonar interference because they rely on sound for communication, feeding, mating and migration. According to the Navy, each of the sonar's 18 speakers transmits signals as loud as 215 decibels, equivalent underwater to standing next to a twin-engine F-15 fighter jet at takeoff.
Environmentalists say, however, that with the convergence of sound waves from each of the speakers, the intense effects of the system would reach farther, as if the signals were 235 decibels.
"The Bush administration has issued a blank check for the global use of this system," said Michael Jasny, a senior policy analyst for the Natural Resources Defense Council. "Today's decision is far too broad to provide any meaningful protection for whales, dolphins and other marine life."
Fisheries officials outlined protective measures calling for Navy personnel to visually scan for marine mammals and sea turtles and to shut down the sonar whenever they are detected. Detection is expected to be almost 100 percent effective from a distance of 1.1 nautical mile away.
The Navy says it will restrict the sonar's routine use to at least 12 nautical miles away from coastline and outside biologically important areas.
The intense low-frequency sonar can travel several hundred miles and the transmissions are on the same frequency used for communication by many large whales, including humpbacks.
Some biologists believe whales are irritated by sounds louder than 110 decibels and that a whale's eardrums could explode at 180 decibels.
Environmentalists' fears are partly based on the Navy's deployment of a powerful mid-range sonar in March 2000 during a submarine detection exercise in the deep water canyons of the Bahamas.
At least 16 whales and two dolphins beached themselves on the islands of Abaco, Grand Bahama and North Eleuthera within hours. Eight whales died. Scientists found hemorrhaging around the brain and ear bones, injuries consistent with exposure to loud sounds.
Twelve Cuvier beaked whales beached themselves in Greece during NATO exercises in 1996 using the low-frequency sonar, but the whales decomposed before scientists could investigate.