The mass grave was found on Thursday and searchers have so far "extracted the remains of 25 unidentified dead people, as well as five bags that are presumed to also contain human remains," the agency said in a statement.
Neighbors said dogs uncovered bones in an abandoned farm, in the town of El Salto south of Guadalajara.
The remains were transferred to a local morgue for further examination.
So far this year, 115 bodies have been found in at least 10 clandestine graves in Jalisco, most of them outside Guadalajara, Mexico's second largest city.
The state has been the scene of rising violence over the past five years, linked to a powerful drug cartel, Jalisco Nueva Generacion.