Justice Minister Sadakazu Tanigaki announced the execution of Tokuhisa Kumagai, who was convicted of shooting dead the owner of a Chinese restaurant in a May 2004 robbery, among other crimes.
The execution was the first since two gangsters were sent to the gallows in April and took place despite repeated protests from European governments and human rights groups.
Japan now has 132 inmates on death row, according to the justice ministry.
Tokyo did not execute anyone in 2011, the first full year in nearly two decades without an execution amid muted debate on the rights and wrongs of a policy that enjoys wide public support.
Apart from the United States, Japan is the only major industrialised democracy to use capital punishment.
International advocacy groups say the system is cruel because inmates can wait for their executions for many years in solitary confinement and are only told of their impending death a few hours ahead of time.
Iwao Hakamada, 77, is believed to be the world's longest-serving condemned inmate.
He was arrested in 1966, accused of the grisly murder of his boss and the man's family. Supporters, who question his guilt, say the long wait has exacted a huge mental toll on him.
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