Land prices at some 370,000 benchmark points across Japan fell an average of 3.1 percent, a smaller fall than the average decline of 4.4 percent the year before, the agency said.
Because the latest assessment of "roadside land prices," which serve as a basis for tax calculations, is dated prior to the March earthquake and tsunami, the agency plans to decide and announce by November adjustment rates for nine stricken prefectures, taking into account disaster-induced falls in their land prices.
Rates reflecting the impact of the calamity will give land owners a tax break.
But real estate dealers are concerned they may spur falling land prices by affecting transactions in disaster areas.
The average percentage change fell in all 47 prefectures for the third consecutive year, but the margin of decline was smaller in 31 of them, centering on the three biggest metropolitan areas of Tokyo, Nagoya and Osaka.
The biggest decline in rate was marked in Kochi Prefecture, at 8.0 percent, followed by 7.2 percent in Tokushima and 5.9 percent in Yamaguchi.
Of the 47 prefectural capitals, only Fukuoka saw an increase in its highest land price, while the highest prices in Nagoya, Nara and Tsu, Mie Prefecture, stayed the same.
Of the 43 other capitals, where the highest land prices sagged, Sendai, Akita and Matsue, Shimane Prefecture, logged double-digit falls.
An area in front of the Kyukyodo stationery store in Tokyo's Ginza shopping district remained the most expensive in Japan for the 26th year in a row at ¥22 million per sq. meter, though it sank ¥1.2 million, or 5.2 percent, from the year before.