Tokyo's ritzy shopping district of Ginza remained one of the world's most expensive areas, with a single square metre of land costing 13.76 million yen ($123,800), up 8.2 percent from a year ago.
Average property prices for the whole of Tokyo, however, fell 2.7 percent to 257,000 yen per square metre, while the nationwide average fell 5.0 percent to 115,000 yen per square metre, the National Tax Agency said.
The agency uses the annual data to levy taxes on property holders.
Japanese land prices are now about a third of their peak hit in 1992. Companies often used land as collateral to borrow from financial institutions, and falling land prices have exacerbated banks' non-performing loans.
Japan's economy is now growing at its fastest pace in over a decade, and corporate sentiment is at its brightest since the bursting of the asset inflated bubble in the early 1990s.
Declines in land prices have been somewhat moderating, with some urban areas showing signs of recovery. But prices remain sluggish overall due to slack demand.