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.
Local neighbors said dogs uncovered bones at 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.
A report by the Mexican government presented on Aug. 30 indicated that since 2006 and until the middle of August 2019, more than 3,000 clandestine graves with at least 5,000 bodies have been found in the country.
The state has been the scene of rising violence during the past five years due to the powerful drug cartel, Jalisco Nueva Generacion.