Scientology's David Miscavige -- Target of Death Threats

Someone is out to kill Scientology honcho David Miscavige ... or so the guy vows, and it's triggered a big police investigation.

A man repeatedly called the main number for Scientology in Hollywood in July, making very direct threats:

"Tell David that we are going to kill him."

"We are going to assassinate Mr. Miscavige and every single one of you."

"You tell your leader, who is an a**hole and a motherf*****, he is going to be shot pretty soon."

We're told the operator kept the man on the phone during the last call for 2 hours and 55 minutes and got identifying information, including his Skype address.

Scientology forwarded the info to LAPD's Major Crimes Unit, which launched an investigation and executed a search warrant last month. The person the LAPD closed in on is a Jewish businessman.