Autophagy is a cellular process that degrades cytoplasmic components to maintain cellular homeostasis during nutrient starvation. In Saccharomyces cerevisiae, the Tor protein kinase suppresses autophagy, but its mechanism is unclear. This study shows that the protein kinase Apg1 is activated by starvation or rapamycin treatment, and its activity is enhanced. Apg13, which binds and activates Apg1, is hyperphosphorylated in a Tor-dependent manner, reducing its affinity for Apg1. This Apg1-Apg13 association is essential for autophagy but not for the cytoplasm-to-vacuole targeting (Cvt) pathway. The Apg1-Apg13 complex plays a key role in switching between the Cvt pathway and autophagy in response to nutrient conditions. The study also shows that Apg13 is phosphorylated by Tor, which reduces its affinity for Apg1, and that dephosphorylation of Apg13 allows Apg1 to activate, leading to autophagy induction. The results suggest that Tor negatively regulates autophagy by hyperphosphorylating Apg13, which reduces the affinity of Apg13 for Apg1. The study also shows that Tap42 does not mediate autophagy induction, indicating that the Apg1-Apg13 complex is involved in a novel Tor signaling pathway that regulates autophagy. The findings suggest that the Tor-Apg1 pathway is conserved in eukaryotic cells.Autophagy is a cellular process that degrades cytoplasmic components to maintain cellular homeostasis during nutrient starvation. In Saccharomyces cerevisiae, the Tor protein kinase suppresses autophagy, but its mechanism is unclear. This study shows that the protein kinase Apg1 is activated by starvation or rapamycin treatment, and its activity is enhanced. Apg13, which binds and activates Apg1, is hyperphosphorylated in a Tor-dependent manner, reducing its affinity for Apg1. This Apg1-Apg13 association is essential for autophagy but not for the cytoplasm-to-vacuole targeting (Cvt) pathway. The Apg1-Apg13 complex plays a key role in switching between the Cvt pathway and autophagy in response to nutrient conditions. The study also shows that Apg13 is phosphorylated by Tor, which reduces its affinity for Apg1, and that dephosphorylation of Apg13 allows Apg1 to activate, leading to autophagy induction. The results suggest that Tor negatively regulates autophagy by hyperphosphorylating Apg13, which reduces the affinity of Apg13 for Apg1. The study also shows that Tap42 does not mediate autophagy induction, indicating that the Apg1-Apg13 complex is involved in a novel Tor signaling pathway that regulates autophagy. The findings suggest that the Tor-Apg1 pathway is conserved in eukaryotic cells.