That was well shy of forecasts for an increase of 4.3 percent, and down from 4.2 percent in August.
The M3 money stock added 3.1 percent to 1,227.2 trillion yen versus expectations for a gain of 3.5 percent and down from 3.4 percent in the previous month.
The L money stock advanced an annual 4.2 percent to 1,624.6 trillion yen.
For the third quarter of 2015, M2 was up 4.0 percent on year, while M3 added 3.2 percent and L advanced 4.5 percent.