Louise Arbour, the U.N. high commissioner for human rights, said the three were executed "suddenly and without advance warning to either the convicts or their families."
"This practice is problematic under international law and I call on Japan to reconsider its approach," she said.
Arbour said she was particularly dismayed by the execution of a 75-year-old prisoner.
"It is difficult to see what legitimate purpose is served by carrying out such executions of the elderly," she said in a statement. "At the very least, on humanitarian grounds, I would urge Japan to refrain from such action."
Arbour noted Japan's decision to release the names of the executed men, breaking with the traditional policy of secrecy surrounding executions in the country.
Japan has routinely faced criticism by human rights activists for keeping details of its executions secret. Until November 1998, the ministry only provided the number of executions in annual statistics.
Arbour said countries have a legal obligation to ensure strict safeguards in their use of the death penalty. It is widely accepted that executions should not be carried out in secret and without forewarning, which may amount to inhuman punishment and treatment under international law, she said.
Japan is one of the last industrialized nations to retain the death penalty, and Arbour urged it to join "the growing number of countries that have implemented a moratorium on executions or banned the practice altogether."
The Justice Ministry's latest available data show 104 more convicts remain on death row.