The final Markit/Nikkei services Purchasing Managers' Index (PMI) for Japan decreased to 51.4 in September from 53.7 in August.
A reading below 50 indicates contraction of activity.
The index was driven by a weaker rise in new orders.
"Despite a weaker expansion in the Japanese service sector, forecasts of output over the next year remained positive," economist at Markit, Amy Brownbill, said.