The population decreased in 40 of the 47 prefectures. Fukushima Prefecture, home of the crippled Fukushima No. 1 nuclear plant, suffered the worst decline at 1.41 percent.
Of the seven prefectures that posted gains, Okinawa topped the list with a 0.56 percent increase.
For the first time, the number of people aged 65 or older surpassed those aged below 14 in every prefecture.
Akita Prefecture had the highest percentage of people 65 and older at 30.7 percent, followed by Kochi at 30.1 percent and Shimane at 30.0 percent.