The unidentified man, described as being in his 40s, approached three guards Sunday in the parking lot of the Scientology Celebrity Centre, Los Angeles Police Deputy Chief Terry S. Hara said.
The man was "close enough to hurt them" when one of the guards shot him, Hara said, and after questioning the guards and looking at surveillance tape decided the shooting was justified.
"The evidence itself, it's very, very clear," Hara said. "The security officers were defending their safety."
Police said the tape showed the man appearing at about noon in a red convertible, then approaching the guards with a sword in each hand before he was shot, Hara said.
The man was later pronounced dead at Los Angeles County-USC Medical Center.
Detective Wendi Berndt told the Los Angeles Times the man had been involved with the church in the past.
"There was a previous relationship, but it is unclear to what degree," Berndt said.
Calls to Scientology spokespeople on Sunday were not returned.
The Celebrity Centre includes a seven-story Norman-revival landmark that towers over the Hollywood freeway and used to be a residential hotel for movie stars.
The castle-like facility now serves as "a home for the artist, a place where he can come and learn, attend seminars, meet other artists and even perform at our many showcases and events," according to the Centre's Web site.
The Church of Scientology was established in 1945 by science fiction writer L. Ron Hubbard and claims 10 million members around the world, including celebrity devotees Tom Cruise and John Travolta.