The preliminary Markit/Nikkei manufacturing Purchasing Managers' Index (PMI) for Japan decreased to 50.9 in September from 51.7 in August.
A reading below 50 indicates contraction of activity.
The index was partly driven by a decline in new export orders, employment and output prices.
"September PMI data pointed to a general slowdown in the expansion of the Japanese manufacturing sector. New order growth moderated, having increased in August at the fastest rate since January. Underpinning the slowdown in total new order growth was a sharp reduction in international demand as new export orders dropped to the greatest extent for 31 months," economist at Markit, Amy Brownbill, said.