The military estimates the training and testing program will have a negligible impact on marine populations.
Navy officials say it's vital to national security that sailors receive sonar training in real-life conditions, and they use simulators where possible.
Environmentalists want the Navy to create safety zones that would guarantee no high-intensity sonar activity near marine sanctuaries and areas with a high concentration of blue, fin and gray whales seasonally.
It calculates more than 11,000 serious injuries off the East Coast and 2,000 off Hawaii and Southern California, along with nearly 2 million minor injuries, such as temporary hearing loss, off each coast. It also predicts marine mammals might change their behaviour such as swimming in a different direction in 27 million instances.
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NMFS granted the permits for the Atlantic and Gulf of Mexico last month. The Pacific permit was the final one. Environmentalists believe the harm will be greater. The California Coastal Commission in March rejected the plan but lacks the power to block the Navy.
Reported mass strandings of certain whale species have increased worldwide since the military started using sonar half a century ago. Scientists think the sounds scare animals into shallow waters where they can become disoriented and wash ashore, but technology capable of close monitoring has emerged only in about the last decade.
Aside from strandings, biologists are concerned that marine mammals could suffer prolonged stress from changes in diving, feeding and communication.