Tokyo's core consumer price index, which excludes fresh food, rose 1.3% in May from a year earlier, marking the slowest pace in four years, according to official government data on Friday.
The reading marks the sixth consecutive month of cooling in the capital.
Excluding both fresh food and energy, the print showed a 1.6% rise compared with 1.9% in April.
Headline CPI, which includes all items, grew 1.4%, slower than the 1.5% rise in April.