Balinda Lee Manley, 34, was arrested Friday.
A department spokesperson said Sheriff Donnie Harrison asked the SBI to investigate after a routine evidence room audit turned up irregularities.
Manley faces one count of possession of marijuana with intent to deliver, one count of embezzling cash, and one count of embezzling marijuana.
The department says the investigation is ongoing.
Manley, of Angier, has been with the sheriff's office since April, 2004.