Justice minister Toshio Ogawa signed the execution orders on Thursday morning and within hours the inmates were taken to the gallows.
One of the men had killed five people at a train station in western Japan in 1999, local media reported.
It is the first time in two years, and only the second time ever, that the left-leaning government has resorted to the death penalty.
Apart from the United States, Japan is the only major industrialised democracy who implements capital punishment.
More than 130 Japanese inmates remain on death row.