Authorities say the facility has not applied for a hardship permit like all the other medical marijuana dispensaries, so selling the marijuana is illegal. About two pounds of marijuana were seized.
The raid came after nearby residents told police illegal drugs were being sold at the location.
Those associated with the temple say it is a Rastafarian ministry, and it has the legal right to sell marijuana to the sick.
"This is a church run medical marijuana club providing medical marijuana for sick people, but we do it as a church," said Pastor Craig Rubin.
"We don't just provide marijuana, we provide for their safety, their security. Every day we give everyone a place to congregate," said Nathan Wade, a member of the Royal Temple of Zion.
Los Angeles police say they acted on several complaints. An officer walked into the facility and watched marijuana stored in mason jars being distributed.
"Once the officer made the observation he notified the northeast station, where the narcotics officers came out, took a look at the location and secured a search warrant," said LAPD Lt. Joseph Satow.
Pastor Rubin believes police are targeting those that have been vocal about legalizing the drug.
"They seem to be particularly picking out people who have applied for these hardships who speak out," said Pastor Rubin.
Members say because this is a place of worship they have not done anything illegal.
"It's because we believe a cannabis from Revelations 22 is a plant for the healing of all nations and that people should have access to this plant. It's not only benign, it's benevolent," said Pastor Rubin.
Police say they are simply being proactive and responding to complaints.
Last week, the LAPD raided two businesses in west Los Angeles that also claimed to be medical marijuana dispensaries.