The California Coastal Commission filed a lawsuit Thursday against the U.S. Navy for rejecting its recommendations for additional safeguards to protect whales and other marine mammals from high-power sonar used by ships in training exercises planned for Southern California waters.

The lawsuit, and a separate suit filed Thursday by environmental and animal welfare groups, sets up a legal battle in federal court in Los Angeles that pits the state’s right to enforce environmental protections against the Navy’s efforts to exempt itself from environmental rules in the interests of national security.

The issue has surfaced because of increasing scientific evidence linking the powerful sonar to panicked behavior of whales and dolphins — and even mass die-offs in the Bahamas, the Canary Islands and elsewhere — after naval exercises.

“The Navy cannot simply arm-wave away the body of evidence that sonar can harm and kill marine mammals,” said Commissioner Sara Wan. She and attorneys for the state and nonprofit groups all said they believe that national security is essential but that extra safeguards for whales and other marine life during training sessions should not compromise troop readiness or national defense.

“Whales and dolphins should not have to die for practice,” said Joel Reynolds, an attorney with the Natural Resources Defense Council.

Vice Adm. Barry Costello, commander of the 3rd Fleet in San Diego, said he was disappointed by the lawsuit but declined to comment on the specifics of the case. He emphasized that the U.S. fleet must be prepared for battle in Asia and the Persian Gulf, including using mid-frequency sonar to hunt for quiet diesel submarines that are proliferating around the world.

“My understanding is that the Coastal Commission didn’t want us to operate our sonar at night,” Costello said. “If we go into harm’s way, our enemy will be working at night. We want to make sure our sailors have the proper training to go forward.”

He said the Navy just wrapped up exercises involving an aircraft carrier and dozens of other ships, aircraft and submarines. All managed to coexist with whales as they have in similar exercises from Santa Barbara to Baja California for the last 30 years, he said.

But this time, to avoid harming marine mammals, the Navy took such precautions as surveying surrounding waters with helicopters before the exercises and adding lookouts on deck and equipping them with night-vision goggles, Costello said. In early preparations for these war games and others, the Navy had also sought the Coastal Commission’s blessing as part of internal guidelines to ensure that major training exercises meet all environmental requirements.

The commission decided not to challenge the training exercises but set a dozen additional conditions, such as avoiding gray whale migratory routes during the seasonal migration and lowering the volume to less-lethal levels at night when whales cannot be easily spotted. The commission has some authority under the Coastal Zone Management Act, a federal law designed to ensure that federal activities don’t violate state environmental programs.

The Navy rejected the extra safeguards last month, saying the commission had no authority to tell it what to do. Furthermore, it said that its sailors were taking sufficient precautions to protect marine mammals, that any behavioral impact on whales would be temporary and that all exercises would occur far enough offshore not to affect state coastal waters or state resources.

Jaimee Jordan Patterson, a state deputy attorney general representing the Coastal Commission, said the Navy’s legal arguments were weak and unlikely to survive federal court scrutiny.

The Navy’s sonar use in training exercises faces other lawsuits filed by the Natural Resources Defense Council, including Thursday’s. The group was joined in that suit by the International Fund for Animal Welfare, the Cetacean Society International, League for Coastal Protection and Jean-Michel Cousteau’s Ocean Futures Society.

The Navy got some relief from litigation this year when the Pentagon granted its training missions a two-year exemption from the Marine Mammal Protection Act, undermining one of the cases. This week the Navy refused to disclose in court the location and dates of upcoming exercises, citing national security.

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