Julio Cesar Martinez, 39, and Anthony Manuel Paez, 32, were charged last week with conspiracy and alteration of evidence by a peace officer while on duty in 2011. Martinez also is charged with perjury and filing a false report. Both are no longer with the sheriff's department.
Each could face more than seven years in state prison if convicted.
They were free on bail Wednesday and it wasn't immediately clear whether they had obtained attorneys.
Martinez and Paez claimed they were on patrol on Aug. 24, 2011, when they saw a drug deal being made and followed a man into the medical marijuana dispensary, prosecutors said.
Martinez claimed he saw the man throw away a gun in an office.
However, prosecutors contend the deputies actually shut off electricity to the room, and that one crawled under the desk and tried to disable the dispensary's video surveillance system. They also allegedly planted handguns in the room one of them next to some Ecstasy pills.
The deputies arrested one man for possession of an unregistered firearm and a second man for possession of a controlled substance while armed with a firearm, authorities said.
"However, when LASD's Internal Criminal Investigation Bureau launched an investigation a year later, they discovered a video recording taken inside the dispensary. Investigators said the video was inconsistent with statements made by the deputies in their reports," according to a statement from the district attorney's office.
The cases against the two arrestees were later dismissed, according to Jane Robison, a spokeswoman for the DA's office.
A call to a representative of the Association for Los Angeles Deputy Sheriffs, the union representing deputies, was not immediately returned.