It rose to 52.6.
Japan's manufacturing Purchasing Managers' Index (PMI) hit a four-month high of 52.6 in September, up from 52.2 in August.
According to IHS Markit, the flash manufacturing output index also grew from 52.5 to 53.5.
This is also the strongest growth in four months.
Export sales also increased at a faster pace, but job creation continued to decline as it reached a 10-month low.
Meanwhile, manufacturers' expectations reflected stronger optimism for the future.
According to IHS Markit principal economist Annabel Fiddes, "Firms signalled stronger expansions in both output and new orders amid reports of firmer demand both at home and abroad."
She added, "The strong end to Q3 bodes well for production in the coming months, with business confidence also perking up slightly since August."
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