The Navy is investigating the incident, but initial reports indicate the mammals had no contact with Perske before he failed to resurface, Fallin said.
The program's nonessential training is on hold during the investigation, Fallin said.
Capt. Kurt Rothenhaus, the Space and Naval Warfare Systems Center Pacific's commanding officer, expressed his condolences to Perske's family, friends and colleagues and called his death a "tremendous loss for us."
Perske had been with the company and the marine mammal program for more than five years, Science Applications International said in a statement.
"Our thoughts and prayers go out to his family and friends," the statement said.
The Navy's $28 million marine mammal program, headquartered in San Diego, trains 80 bottlenose dolphins and 40 California sea lions to do everything from finding underwater mines to stopping enemy divers.
Marine mammals have been used during wartime from Vietnam to Iraq.
The sonar of bottlenose dolphins make them highly effective at finding underwater mines, which are hard to detect. California sea lions can see extremely well in darkness, have directional hearing and can squeeze through tight spaces — which makes them effective at marking and retrieving objects in the ocean. Both species can make repeated deep-water dives, unlike humans.
The mammals are not trained to attack and are never used to harm people, according to the Navy. They are trained to intercept swimmers and can carry devices to attach to anyone posing a threat so sailors can then either reel them in or go in to respond appropriately.
The Navy's marine mammals also never have to carry potentially catastrophic mines but instead find the devices and place markers near them. They are then removed from the area before Navy divers retrieve and defuse the devices.