Year-on-year, prices of transport and communication recorded the highest decrease (-2.4 percent), followed by fuel, light and water charges (-1.7 percent) and housing (-0.1 percent).
Upward pressures came mainly from cost of food (up 3.1 percent), clothing and footwear (up 1.8 percent), education (up 1.5 percent) and recreation and culture (up 0.7 percent).
Core consumer prices including oil products but excluding fresh food rose 0.1 percent in May from a year earlier, slowing from a 0.3 percent increase in April and much below the central bank's 2 percent target. The so-called core-core inflation which excludes food and energy prices rose 0.4 percent, the same rate as in April.
On a monthly basis, the inflation rate eased to 0.3 percent in May from 0.4 percent in the previous two months.
In Tokyo, consumer prices rose at a slower pace of 0.3 percent year-on-year in June (0.5 percent in May). Monthly inflation fell to -0.4 percent from 0.1 percent in the previous month.