The three men were senior officials at Tokyo Electric Power Company (TEPCO), the operator of the Fukushima Daiichi plant, and had faced up to five years in prison if convicted.
The men -- Tsunehisa Katsumata, 79, Sakae Muto, 69, and Ichiro Takekuro, 73 -- were accused of professional negligence resulting in death and injury for failing to act on information about the risks from a major tsunami, but they argued the data available to them at the time was unreliable.
"The lawyers filed an appeal today," a Tokyo District Court spokeswoman told AFP.
An online petition demanding an appeal was launched following the acquittal ruling of last week and more than 13,500 people have signed.
The presiding judge said that the verdict turned on the "predictability" of the massive tsunami that swamped the nuclear plant in March 2011 after a 9.0-magnitude undersea earthquake.
No one was killed in the nuclear meltdown, but the tsunami left 18,500 dead or missing.
The ex-TEPCO executives faced trial in relation to the deaths of more than 40 hospitalised patients who died after having to be evacuated following the nuclear disaster.
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