By mid-1993 Núñez Soto had moved to the state of Hidalgo to join the cabinet of governor Jesús Murillo Karam as secretary of industry and commerce. In 1995 he took over the state Secretariat of the Interior and two years later he was elected to the Chamber of Deputies representing Hidalgo's sixth district (the city of Pachuca and surrounding areas).[1]
After two years in the Chamber Núñez Soto resigned to become the PRI candidate to the governorship of Hidalgo. He won the election in 1999 and served in the post until April 2005. During his administration the employment rate grew 18% and the agricultural production grew 52%.
During the early months of 2005 Núñez Soto sought the 2006 PRI presidential candidacy.