Mr Eitan suggested Mahmoud Ahmadinejad could be brought to trial
Iran has protested to the UN after an Israeli minister suggested his country could kidnap Iran's president over threats he has made against Israel.
Iran's UN ambassador called the remark "outrageous and vicious" and called on the UN Security Council to take action.
Israeli minister Rafi Eitan suggested President Mahmoud Ahmadinejad could be kidnapped and brought to trial.
Mr Eitan, an ex-intelligence chief, was involved in the kidnap of leading Nazi Adolf Eichmann in Argentina in 1960.
In an interview with the German magazine Der Spiegel, Mr Eitan suggested that such an operation could be staged to bring Mr Ahmadinejad before the International Criminal Court in The Hague.
The Iranian leader has made a number of threats against Israel, repeatedly predicting the state will soon disappear.
Mr Ahmadinejad also drew international rebuke by quoting the view of the late Iranian spiritual leader, Ayatollah Khomenei, that Israel was a tumour that needed to be erased from history.
In a letter to UN Secretary General Ban Ki-Moon, the ambassador Mohammad Khazee said Mr Eitan's remarks reflected Israel's "aggressive and terrorist nature", Iran's Irna news agency reported.
"These dangerous threats of resorting to criminal acts against the officials of a sovereign country, or threatening to use force against a member of the United Nations not only constitute manifest violations of international law and contravene the most fundamental principles of the Charter of the United Nations, but are against the basic values of the civilised world," he said.
Mr Khazee said such remarks demanded "a resolute and clear response" by the UN and its security council.
Iran, he said, had never threatened any other nation but "would not hesitate to act in self-defence to respond to any attack against its territory or its people".
Israel has expressed increasing concern about what it considers to be a threat from Iran's nuclear programme and recently suggested it might resort to military force to stop it.
Iran has insisted its nuclear ambitions are solely peaceful.