The hangings brought to seven the number of death row inmates executed during the regime of Prime Minister Yoshihiko Noda.
Those hanged Thursday were identified as Sachiko Eto, 65, a faith healer convicted of killing four believers in 1994 to 1995 and killing two others, and Yukinori Matsuda, 39, convicted of robbery and killing two people in 2003.
Last month, when two others were executed, Amnesty International condemned the actions. Three others had been executed in March.
"After carrying out no executions in 2011, Japan has put five people to death this year firmly reestablishing itself in the minority of countries who still use capital punishment," said Roseanne Rife, AI's special projects head.
Rife said Japan's leadership is "choosing to hide behind public opinion rather than demonstrate leadership and work towards the abolition of this ultimate cruel, inhuman and degrading punishment."
Britain's The Guardian newspaper, while reporting the March executions, said none of the 132 people on Japan's death row was executed in 2011, the first such in 19 years when no inmate was hanged.
The Guardian said Japan is one of 58 countries including the United States, China and Iran where capital punishment is allowed, while more than 140 countries, including all European Union members, have abolished the death penalty.