The Ministry of Finance is offering 700 billion yen ($8.9 billion) of 30-year bonds with a 2.0 percent coupon, reopening the number 36 issue.
Growing investor risk tolerance also reduced the appeal of fixed-income assets as hopes rose for progress on rescuing Spain's debt-laden banks.
German officials said on Wednesday that European officials are urgently exploring ways to prop up Spain's lenders, including ways that might avoid imposing the kind of painful austerity requirements that cast other bailout deals into political peril.
"Worries about Spain have faded since Monday, and it was those fears, combined with worries about the US economy after the jobs data, that sent yields to historic lows," said a fixed-income fund manager at a Japanese asset management firm.
On Monday, the benchmark 10-year yield dropped to a nine-year low of 0.790 percent, but bonds sold off after a 10-year JGB auction on Tuesday drew only tepid demand, and then rallied back on Wednesday afternoon on bargain-hunting.
The yield curve steepened as superlongs underperformed ahead of the 30-year sale, with the 30-year yield adding 3 basis points to 1.865 percent, its highest level in five weeks.
The 20-year yield added 2 basis points to 1.690 percent, while the five-year yield was flat at 0.210 percent.
The 10-year JGB yield rose 1.5 basis point to 0.880 percent, while 10-year JGB futures ended morning trade down 0.18 point at 143.41.