The conflict in "The Master Puppeteer" is a man versus society conflict. In the feudal system that provides the setting, there is a clear delineation between those who have and those who do not. As Isako explains, everything "goes to the daimyo or the tax collector...a farmer's children starve while the rice brokers grow fat" (Chapter 16). Culture dictates that the starving mask their suffering for politeness's sake - thus, Jiro is expected to decorously decline an offered meal at Yoshida's table (Chapter 2), even though he is so hungry that his hands shake when he works on his father's puppets and he fanticizes about eating the glue used in their construction (Chapter 1). Poverty and hunger are the driving forces underlying the motivations of the characters. The boys at the Hanaza Theater treasure their apprenticeship because it keeps them from starvation, and the desperate mobs in the streets become increasingly enraged as they struggle to survive in the face of gross inequity.
The symbol of the story's central conflict is Saburo, the Robin Hood-like character who is the only one who has managed to defy society's hierarchies with impunity. Using brilliantly planned schemes and disguises like the incident where a group of monks gains access to the rice brokerage in Yamamoto (Chapter 3), Saburo essentially steals from the rich to give back to the poor, capturing the imagination and giving hope to the downtrodden masses.