The decision comes after prosecutors twice refused to press charges against the men, saying they had insufficient evidence and little chance of conviction.
But the independent panel on Friday ruled - for the second time since the accident - that the executives should be put on trial, compelling prosecutors to press on with the criminal case under Japanese law.
The decision is the latest in a tussle between legal authorities and the public over who should take responsibility for the tsunami-sparked reactor meltdowns that forced tens of thousands from their homes in the worst nuclear accident since Chernobyl.
The trio are former Tokyo Electric Power chairman Tsunehisa Katsumata, then-vice president Sakae Muto and former vice president Ichiro Takekuro.
“The victims have wanted a criminal trial given the anger and grief” over the accident, Ruiko Muto, a campaigner who called for charges, told reporters.
“We feel a sense of achievement that a criminal case will be held to account for an accident that caused such tremendous damage.” The judicial panel is composed of ordinary citizens.