Several law enforcement officers are on leave pending the investigation, Eyewitness News has also learned.
And about a dozen weapons are still missing, sources say.
The civilian manager of the gun store, 33-year-old Archi Duenas, was arrested for grand theft on March 19, according to the LAPD.
Duenas is not an employee of the Los Angeles Police Department. The gun store at the academy is run by the nonprofit Los Angeles Police Revolver and Athletic Club.
The LAPD says the alleged theft was discovered during a routine audit of sales by LAPRAAC management.
The investigation continues.
The gun store is currently closed under Mayor Eric Garcetti's stay-at-home orders spurred by the coronavirus pandemic.