“The company has relieved Dr Bruno Thomauske of his duties,” Vattenfall, a Swedish-owned firm, said in a statement.
It added that the communications chief for VENE, Johannes Altmeppen, had resigned.
Thomauske’s departure follows problems at the Krümmel and Brunsbüttel nuclear power plants in northern Germany in late June.
German officials have accused the company of failing to report the full extent of a fire at the Krümmel plant and neglecting for days to inform authorities of problems operators experienced at nearby Brunsbuettel after the plant had to be shut down because its capacity was overloaded.
Vattenfall said it would assemble a team of experts “this week still” to analyse operations in Germany and to suggest how they could be improved.
“We will implement their recommendations to the letter. The aim is to remove any doubt about security at the plants and about operational procedures,” it added.
The company has denied that it sought to cover up the extent of the problems at the two plants.