Consumer prices fell 1.1% in May from the same month a year ago, the most since records began in 1970.
Prices of goods excluding fresh food also fell for the third straight month.
Japan was previously trapped in a deflationary spiral, where prices of goods kept falling, during its "Lost Decade" in the 1990s.
"We must carefully manage the economy so that it does not collapse further and enter into a deflationary spiral," Japan's Finance Minister Kaoru Yosano said.
Deflation damaging to an economy because consumers tend to delay making purchases until prices fall further. This in turn drives down prices more.
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