Russia seized the Zaporizhzhia plant in southern Ukraine soon after invading the country in February.
"Yesterday ... the Russian military broke into the premises of the social programmes department and... severely beat the department head Oleksiy Trubenkov and his deputy Yuriy Androsov," Ukraine's nuclear agency Energoatom said.
"After a brutal beating, the invaders took them out of the premises in an unknown direction," the state-run company said.
Energoatom said Russia "intensified repression" against the facility's staff.
Earlier this month, Ukrainian engineer Yuri Chernichuk agreed to become the new head of plant under Russian nuclear operator Rosenergoatom's authority.
He was branded a traitor by Kyiv and formally sacked.
Energoatom head Petro Kotin told AFP in September that Russian forces had tortured staff at the nuclear power station, and that at least two people had been killed.
He has also said that plant employees had been kidnapped "periodically".
Russia and Ukraine have for months accused each other of shelling around the plant.
The UN's atomic watchdog in November denounced strikes on the plant's territory, calling for a "stop to this madness."
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