File photo: Russia s foreign ministry spokeswoman Maria Zakharova (Reuters)
Eliyahu's remarks, from which which he later backtracked, prompted outrage and led to his suspension.
"We find these statements to be provocative, totally unacceptable," foreign ministry spokeswoman Maria Zakharova said.
"Such statements imply that the entire population of the Gaza Strip is being threatened with nuclear weapons... Is that a threat of genocide?"
Eliyahu had told Israel's Kol Barama radio that he was not entirely satisfied with the scale of Israel's retaliation.
He responded to a question by saying dropping some kind of atomic bomb would be "one option" but later said his statement was "metaphorical."
Israel is widely known to have nuclear weapons but has never admitted so.
"These statements not only clearly confirm the country's possession of such weapons but also demonstrate its readiness to seriously consider their use in completely inappropriate scenarios," Zakharova said.
Russian President Vladimir Putin has criticised the West for allegedly stoking tensions in the region and Israel for its conduct in the conflict.