The Justice Ministry reportedly confirmed the men, all executed for murder, were:
- Shojiro Nishimoto, 32, hanged at the Tokyo Detention Center
- Yukinari Kawamura, 44, and Tetsuya Sato, 39, hanged in Nagoya
- Tadashi Makino, 58, hanged in Fukuoka.
"These are heinous cases which destroyed precious human lives," justice minister Mori Eisuke said, according to a report by AFP newsagency.
"I ordered the executions after cautious examination."
Mori Eisuke has now sent six men to the gallows since he was appointed justice minister on 24 September 2008.
He previously approved two executions, with the hanging of Michitoshi Kuma, 70, and Masahiro Takashio, 55, on 28 October.
The Japanese section of Amnesty International condemned the latest executions.
"We feel strong anger over these executions," the organisation's Tokyo branch said in a statement quoted by AFP.
"The Japanese government should recognise its international obligation to establish a criminal justice system which does not rely on capital punishment"
Japan executed a total of fifteen people in 2008, the highest rate in more than thirty years.
Executions in Japan -- 2006 - 2008 -- 2 January 2009
Japan may execute before year ends -- 16 December 2008
Japan: Record toll with new hangings -- 28 October 2008
Japan: New minister faces next hanging -- 14 October 2008
Japan: New minister sends three to death -- 12 September 2008