Ex-Tokyo Electric Power (TEPCO) chairman Tsunehisa Katsumata, then-vice president Sakae Muto and former vice president Ichiro Takekuro were formally charged with professional negligence resulting in deaths and injury.
The trio were not taken into custody.
"We were notified from our lawyers that the three were indicted," a spokeswoman for a campaign group pushing for a trial told AFP.
A judicial review panel composed of ordinary citizens ruled in July -- for the second time since the accident -- that the trio should be put on trial.
Prosecutors had twice refused to press charges against the men, citing insufficient evidence and little chance of conviction.
It will be the first criminal trial over responsibility for the tsunami-sparked reactor meltdowns that forced tens of thousands from their homes in the world's worst nuclear accident since Chernobyl in 1986.
Public broadcaster NHK said the three would plead not guilty, arguing it was impossible to predict the size of the massive tsunami that slammed into Japan's northeast coast.
Although the March 11 earthquake and tsunami killed 18,500 people, the nuclear disaster it caused is not officially recorded as having directly killed anyone.
Around a dozen others -- including TEPCO employees and members of Japan's Self Defense Forces -- were injured during the accident.
Environmental group Greenpeace said the decision to press on with a criminal case was "a major step forward".
"The court proceedings that will now follow should reveal the true extent of TEPCO's and the Japanese regulatory system's enormous failure to protect the people of Japan," said Hisayo Takada, deputy programme director at the organisation's Japan office.
It pointed to weaknesses in disaster preparedness and in plant design, along with unclear responsibilities among regulators.
A 2012 parliamentary report also said Fukushima was a man-made disaster caused by Japan's culture of "reflexive obedience", but no one has been punished criminally.
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