The final Markit/Nikkei manufacturing Purchasing Managers' Index (PMI) for Japan decreased to 51.0 in September from 51.7 in August, up from the preliminary reading of 50.9.
A reading below 50 indicates contraction of activity.
The index was driven by declines in exports and purchasing activity.
"Growth in production at Japanese manufacturers eased further in September to the weakest rate in the current five-month sequence of expansion," economist at Markit, Amy Brownbill, said.
She added that the decline in exports was driven by lower trade volume with China.