Public broadcaster NHK and other Japanese media reported that the trio were put to death in the early morning hours today without giving further details or identifying the condemned prisoners.
The justice ministry did not immediately confirm the reports but Justice Minister Sadakazu Tanigaki was to hold a press briefing at 0730 IST.
If confirmed, the executions would be Japan's first since two death-row inmates were hanged in September under a centre-left Democratic Party of Japan government.
Japan did not execute any condemned inmates in 2011, the first full year in nearly two decades without an execution amid muted debate on the rights and wrongs of a policy that enjoys wide public support.
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But in March last year, Tokyo resumed its use of capital punishment with an unapologetic government minister signing death warrants for three multiple murderers.
Apart from the United States, Japan is the only major industrialised democracy to carry out capital punishment, a practise that has led to repeated protests from European governments and human rights groups.