The two-year yield was unchanged at -0.040 percent , the benchmark 10-year yield rose half a basis point to 0.275 percent and the 40-year yield fell a basis point to 1.380 percent.
The two-year yield has spent much of the past six weeks below zero percent, hitting a record low of -0.060 percent last week, driven steadily lower under the Bank of Japan's debt-buying scheme.
Tuesday's 2.5 trillion yen ($20.62 billion) two-year sale underlined strong investor demand. The yield on the lowest accepted price was -0.009 percent and the yield on the average accepted price was -0.013 percent, both record lows.
The Nikkei was down 0.1 percent, on track for its second day of losses, hurt by concerns stemming from declining crude oil prices and uncertainty over how the Federal Reserve's interest rate hike would impact risk appetite.