A 12.4% decline in auto-related production - the sector's steepest fall in eight months - drove down the overall index.
Manufacturers surveyed by the Ministry of Economy, Trade and Industry (METI) expected output to fall another 0.4% in October and rise 0.8% in November.
"Rather, with rising procurement costs on the weak yen, coupled with (higher) energy prices, some firms have voiced concerns for their business conditions."
Separate data showed retail sales rose 4.5% year-on-year in September, extending a rebound since March when the government ended domestic COVID-19 containment measures.
On a seasonally adjusted month-on-month basis, retail sales grew 1.1% in September, rising for a third month.