"EON will sue over the nuclear fuel rod tax," the group said in a statement.
The levy on nuclear energy production was agreed with the government last year in exchange for an extension of the reactors' lifetime.
Retaining the tax while the reactors' lifespan is being greatly reduced was unfair, the company said.
"I reckon that the politically motivated reduction of the plants' lifespan will entail losses of several billion euros," EON boss Johannes Teyssen told the daily Frankfurter Allgemeine Zeitung.
EON shareholders should not bear the cost alone, he said, in an interview to be published Wednesday.
"The cost of the energy overhaul must be borne by society as a whole," he added.
The government wants to retain the tax, amounting to about €2.3 billion per year, despite its decision announced Monday to shutter all 17 of Germany's nuclear reactors within 11 years.
Eight have already been closed and will not reopen.
EON, one of four energy companies currently operating nuclear plants in Germany, said retaining the tax over the next decade would also reduce its ability to invest in renewable energies, which are needed to replace nuclear power, and would penalise it compared to European competitors.