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The five-year JGB yield fell 1 basis point to minus 0.165 percent and the 10-year yield dipped half a basis point to minus 0.015 percent.
The BOJ on Thursday offered to buy 430 billion yen ($3.87 billion) of five- to 10-year JGBs, which was unchanged from its previous operation last week.
The central bank had caught investors off guard earlier in the week when it trimmed the amount of 10- to 25-year JGBs it offered to buy, causing longer-dated bonds to sag.
The BOJ often tweaks the amount of JGBs it buys at market operations as a part of its yield curve-controlling scheme.
JGB price gains, however, were limited following a retreat by U.S. Treasuries and as Japanese shares advanced to a two-month high.