The hangings of Masakatsu Nishikawa and Koichi Sumida bring to 19 the total number of executions since conservative Prime Minister Shinzo Abe came to power in late 2012.
Nishikawa, 61, was convicted of killing four female bar owners in western Japan in 1991, while Sumida, 34, was sentenced to death for killing a female colleague in 2011 and dismembering her body.
"Both are extremely cruel cases in which victims were deprived of their precious lives on truly selfish motives," Justice Minister Katsutoshi Kaneda said.
"I ordered the executions after careful consideration," he told a news conference.
Human rights group Amnesty International protested at the Japanese government's continued use of the death penalty, saying it demonstrates "wanton disregard for the right to life".
"The death penalty never delivers justice, it is the ultimate cruel and inhumane punishment," Hiroka Shoji, East Asia researcher at the campaign group, said in a statement.
Nishikawa was hanged while seeking a retrial. Though not unprecedented, it is rare in Japan.
"When a rejection is naturally expected, we cannot help avoiding carrying out [capital punishment]," Mr Kaneda said, noting he was not commenting on either of the cases but speaking in general terms.
Out of 124 death-row inmates, 91 are seeking retrial, according to Jiji Press.
Japan and the United States are the only major developed countries that still carry out capital punishment.
Government spokesman Yoshihide Suga said "the justice minister made the decision appropriately under the provision of the law".
The death penalty has overwhelming public support in Japan despite repeated protests from European governments and human rights groups.
Opponents say Japan's system is cruel because inmates can be on death row for many years in solitary confinement and are only told of their impending execution a few hours ahead of time.