Core consumer prices rose 2.3 percent in September from a year earlier, up for a 12th straight month, official figures showed.
But they increased at a slower pace than in August, when inflation hit 2.4 percent, the fastest since October 1997.
Japan was trapped in a deflationary spiral for years, but the return of inflation has also caused concern because it is being driven by rising import costs rather than a stronger domestic economy.
A recent drop in the price of oil and other commodities now appears to be dampening inflationary pressures, even if energy costs are still higher than a year ago.
Compared with the previous month, core prices rose just 0.2 percent in September.
"The pace of increases in the cost of electricity, kerosene and gasoline slowed," the Ministry of Internal Affairs said in a statement.
But at the same time price increases for food picked up, it said.
Core inflation in Tokyo, a leading indicator released a month earlier than the figures for