"This is the opposite of what this conference seeks to achieve," he said.
"I reminded the president that the UN General Assembly had adopted the resolutions to revoke the equation of Zionism with racism and to reaffirm the historical facts of the Holocaust respectively".
The United States condemned Ahmadinejad's speech as "vile and hateful".
"I can't think of any other word than shameful," Alejandro Wolff, Washington's deputy UN ambassador, said.
"It does a grave injustice to the Iranian nation and the Iranian people, and we call on the Iranian leadership to show much more measured, moderate, honest and constructive rhetoric when dealing with issues in the region," he said.
Benyamin Netanyahu, the Israeli prime minister, said the Iranian president's comments showed anti semitism still exists.
"The sad fact is that as we commemorate the events of the holocaust here in Yad Vashem, Jerusalem, there are those who have chosen to participate in the demonstration of hatred against Israel and Jews in the heart of Europe," he said, addressing a gathering commemorating the victims of the Holocaust.
Some 23 European Union delegates walked out of the conference hall in Geneva on Monday after Ahmadinejad criticised the creation of a "totally racist government in occupied Palestine".
A number of Western countries, including the United States and Germany, had already boycotted the summit over fears that the Iranian president would use it as a platform to oppose Israel.
The Czech Republic announced it would also boycott the summit, in reaction to Ahmadinejad's speech.
A foreign office statement said: "The Czech Republic is making a definitive withdrawal from the 'Durban II' review conference against racism in Geneva, as a
response to anti-Israel declarations made by the Iranian president, which treated Israel as having a racist government".
"As with our democratic partners, EU and non-EU members, we cannot allow (ourselves) to legitimise with our presence ant-Israeli attacks which are totally unacceptable," it said.
Jonas Gahr Store, Norway's foreign minister, said Ahmadinejad's words amounted to incitement to hatred.
"Norway will not accept that the odd man out hijacks the collective efforts of the many," he said.
Peter Gooderham, a British diplomat, described the speech as "anti-Semitic" and said they "should have no place in a UN anti-racism forum".
Rupert Colville, spokesman for Navi Pillay, the UN high commissioner for human rights who convened the meeting, said the speech was "completely inappropriate at a conference designed to nurture diversity and tolerance".