Police were called Sunday to the Montage Resort and Spa by a security guard who said a man and a woman were engaged in a domestic dispute, said police Sgt. Jason Kravetz.
Several subsequent 911 callers said a naked woman was running around the hotel waving a gun, authorities said.
Police arrived at the pair's room minutes later, and a gun was passed between the man and the woman, who both pointed it at police, authorities said.
Two officers fired into the room after the couple refused to drop the gun.
Police searched the room after the shooting and found a loaded semiautomatic handgun and extra ammunition.
The deaths were the first homicides in Laguna Beach in nearly four years, Kravetz said.
"For something like this to happen here is an anomaly, especially at that location," he said. "It's a very quiet community."
The 262-room resort hotel opened in 2003 and is popular with celebrities.
Bungalows like the one where the couple was found rent for $2,200 a night, according to the hotel's Web site.
The names of the dead were withheld pending notification of their relatives.
The case has been referred to the Orange County district attorney's office, which investigates all officer-involved shootings.