Three of the deaths came after a blast during Navy exercises. The National Marine Fisheries Service says the Navy may also be responsible for two other dolphin deaths.
The agency is going to take another look at the Navy's pending request to disturb marine mammals.
The Navy conducts amphibious and special warfare training between Imperial Beach and Coronado.
The Navy's application has been in the works for years and says it does not anticipate any dolphin deaths due to training, but the fisheries service has opened an enforcement case that will seek to determine whether the Navy has violated the Marine Mammal Protection Act of 1972, a landmark law designed by Congress to safeguard dolphins, whales and similar creatures.
Environmentalists have called on the Navy to suspend activities involved in the deaths and conduct a transparent investigation.
But Navy officials said the program it calls "mission-critical" would continue. They said they were following proper procedures on the day of the blast and are conducting their own investigation to see if changes are necessary.
The Associated Press contributed to this report.
