Iran says it has no intention to attack Israel despite a call by its president to have it "wiped off the map".
Mahmoud Ahmadinejad says he speaks for his people
Iran's foreign ministry said Tehran respected the UN charter and had never used or threatened to use force.
But it also rejected a UN Security Council statement condemning President Mahmoud Ahmadinejad over his comments.
An Iranian TV channel broadcast the remark for the first time on Saturday, saying reaction to it was coordinated by Israel in a plot against Iran.
Mr Ahmadinejad made the controversial comments during a speech to students in Tehran on Wednesday.
They were seen by the outside world as a threat and the latest reaction from Iran is an effort to calm the outcry, says the BBC's Frances Harrison in Tehran.
Our correspondent says this is the closest Iran has come to saying it will not attack Israel.
Israel - which had demanded the emergency Security Council meeting - welcomed Friday's statement.
"The Security Council condemns the remarks about Israel attributed to Mr Mahmoud Ahmadinejad, President of the Islamic Republic of Iran," said the declaration, agreed by all 15 members.
But reacting to the statement on Saturday, Iran's foreign ministry insisted it had no intention of attacking Israel.
It went on: "The declaration published by the Security Council - proposed by the Zionist regime to cover its crimes and give an image at odds with reality - is unacceptable."
It expressed surprise that the Council had never condemned threats made against Iran by the US and Israel or the "crimes" of the Israeli regime.
Ahead of the UN session demanded by Israel, President Ahmadinejad stood by his "just" remarks.
He attended the Jerusalem Day rally in Tehran which Iran organises every year to show solidarity with the Palestinian struggle.
Thousands of Iranians attended an anti-Israel rally on Friday
Mr Ahmadinejad said: "My words were the Iranian nation's words.
"Westerners are free to comment, but their reactions are invalid."
Palestinian chief negotiator Saeb Erekat has distanced the Palestinian leadership from the Iranian position.
Iranian officials have said there was nothing new about the president's comments, which quoted a slogan of the 1979 Islamic revolution.
They have blamed the foreign media for blowing the crisis out of proportion and accused the West of seizing on this issue to pressure Tehran over its nuclear programme.
But there is no doubt this incident has damaged Iran's standing internationally at a time when the country badly needs support to prevent its nuclear dossier being referred to the UN Security Council, our Tehran correspondent says.