Western states are wary of Mr Ahmadinejad's impending address
Israel has recalled its ambassador to Switzerland "for consultations" amid ongoing controversy over an anti-racism conference being held in Geneva.
The protest came as the UN conference was due to be addressed by Iranian president Mahmoud Ahmadinejad, who has described the Holocaust as a "myth".
The US, Australia and Germany are among countries boycotting the talks, but France and the UK are attending.
UN Secretary General Ban Ki-moon has expressed dismay at the boycotts.
Israeli officials were reported to be angered by a meeting between Swiss President Hans-Rudolf Merz and Mr Ahmadinejad on the sidelines of the conference.
The office of Israeli Prime Minister Benjamin Netanyahu issued a statement saying that he and Foreign Minister Avigdor Lieberman had decided to recall Ambassador Ilan Elgar from Berne "for consultations and in protest at the conference in Geneva", Reuters reported.
World affairs correspondent, BBC News website
The one issue that never seems to go away when conferences of this kind are held is the Israeli-Palestinian one.
A document has been already been agreed among those governments attending and you have to read it quite closely to detect the tremors remaining from the earthquakes in discussions that went before.
But enough contentious issues remain and the result is a boycott by the US, Israel, Germany, Italy, Australia, Canada and New Zealand.
The conference coincides with Holocaust Remembrance Day in Israel, which begins at sundown on Monday.
In comments broadcast on Israeli media, Mr Netanyahu said: "Six million of our people were slaughtered in the Holocaust.
"While we commemorate them, a conference purporting to be against racism will convene in Switzerland. The guest of honour is a racist, a Holocaust-denier who makes no secret of his intention of wiping Israel off the face of the earth."
As the controversy continued, UN chief Ban Ki-moon was reported to be meeting Mr Ahmadinejad, hours before the Iranian leader was due to address the conference.
"I confirm (the meeting). Yes, at this moment," the UN spokeswoman in Geneva, Marie Heuze, told AFP news agency, declining to give further details.
Mr Ban told the opening session he was "profoundly disappointed" at the boycotts.
"There comes a time in the affairs of humankind when we must stand firm on the fundamental principles that binds us," he said. "There comes a time to reaffirm our faith in fundamental human rights and dignity and worth of us all, a time to give the virtues of tolerance in respect for diversity their fullest due and look beyond a past that divides us towards a future that unites us. The time is now, ladies and gentleman. The time is now."
The UN's first conference on racism in the South African city of Durban eight years ago was marred by anti-Semitic comments from some non-governmental organisations.
There was also an unsuccessful attempt by some states to equate Zionism with racism.
Now, many Western countries are uncomfortable with the address by Mr Ahmadinejad, the only major leader to accept an invitation to the forum.
Ban Ki-Moon expresses 'regret' that some nations are boycotting the conference
His presence at a conference against racism has caused horror in Israel, and nervousness within the United Nations, says the BBC's Imogen Foulkes in Geneva.
If Mr Ahmadinejad uses the conference to repeat attacks on Israel, or even to deny the Holocaust, it will be a disaster for an event the UN had hoped would be a shining example of international unity against discrimination, our correspondent says.
The five-day Durban Review Conference in Geneva - or Durban II - is the UN's first global racism conference in eight years.
The draft final declaration, which has been causing much heated debate, has been watered down to remove all references to Israel and the Middle East.
However, at the request of Middle East nations, it still contains a clause about the incitement of religious hatred, which many Western countries see as a curtailment of free speech.
US President Barack Obama said anti-Israeli language in the draft final communique that was "oftentimes completely hypocritical and counterproductive" had been the red line for his administration.
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