Summer Collins and Michelle Maloney now have warrants out for their arrests.
Corrections director Jerry Collins says the jail is already making changes.
Some of the newest staff members at Louisville's jail have fur and four legs.
Investigators said they found nearly 60 pills and something else: suspected fentanyl, leading to another arrest.
Kentucky State Police made the arrest on Thursday.
Authorities estimated the value of the shipment at nearly $130,000.
Officials said the two left contraband at a work site for offenders. The inmates who worked at the site then were expected to smuggle the contraband into the jail.
Police have been looking for 41-year-old Matthew Bays since November.
The Clark County Sheriff's Office says 10 inmates were involved in the plot.
Authorities say the burrito was not filled with rice and beans.