Three, perhaps four, dolphins, died in 2011 during a Navy training exercise involving underwater explosives near San Diego.
The area had been cleared but dolphins moved in too late for divers to be able to turn off a charged timer, Stone said. "The dolphins were at the wrong place at the wrong time."
After the incident, the size of the mitigation area was increased.
"We learned from this lesson and moved forward," Stone said.
"The limited impacts we are expecting are to individual animals, not to the species population," he said.
Smith, of the Natural Resources Defense Council, said the National Oceanic and Atmospheric Administration is trying a different approach.
The agency is identifying marine mammal "hot spots" with a high population density, Smith said. The Navy, he said, should do a better job of not using disruptive sonar and explosives in such zones.
Van Name said the Navy already identifies areas for special protection, including a humpback whale sanctuary off Maui. Crews also are aware of calving season and areas.
The Navy is seeking public input over the next 60 days as it moves forward in the permit process.
"We encourage the public to engage with us so we can do a better job," Van Name said. "This document is very robust, very defensible and people will see that."
While the Navy's chief mission is defending the country, it has "a long history of environmental stewardship," Van Name said.