The executions were the fourth and fifth since the Liberal Democratic Party of Prime Minister Shinzo Abe returned to power in December, Kyodo News reported. Three death row inmates were hanged in February.
The Justice Ministry said the two executed Friday had been convicted in the 2005 gunning down of two men linked to a rival crime syndicate in a restaurant in Ichihara in Chiba Prefecture.
There were no hangings in Japan in 2011. At the end of last year, the ministry said there were 133 inmates on death row, the highest number since 1949.
Japan is one of the 32 nations that have the death penalty. U.N. figures show about 150 nations have either abolished the death penalty or do not practice it.