Overall consumer prices in the Tokyo area were up 0.2 percent on year in September, the Ministry of Internal Affairs and Communications said on Tuesday.
That was shy of expectations for an increase of 0.3 percent, which would have been unchanged from the August reading.
Core CPI, which excludes volatile food prices, slipped an annual 0.2 percent. That exceeded forecasts for a drop of 0.3 percent, which also would have been unchanged from the previous month.
On a seasonally adjusted monthly basis, overall Tokyo inflation was down 0.1 percent and core CPI was flat.
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