US State Department Spokesman Robert Wood announced that despite improvements from an earlier draft, the changes in the final text do not address US concerns about anti-Israel and anti-Western bias.
The administration had lobbied hard for more revisions so that it could participate.
The Israel and Canada are not attending over concerns about a possible repeat of verbal attacks on the Jewish state.
The five-day meeting to be held in Geneva is intended to evaluate progress toward goals set by the first such conference in 2001.
During that meeting, the United States and Israel walked out midway through the conference over a draft resolution that singled out Israel for criticism and which likened Zionism - the movement to establish a Jewish state in the Holy Land - to racism.
Many of the same issues are now re-emerging in this latest meeting of the World Conference Against Racism, Racial Discrimination, Xenophobia and Related Intolerance.
The European Union has not decided on whether to attend the meeting or boycott it over Islamic nations' demands to condemn Israel.
"We have made clear that we cannot tolerate it if this anti-racism conference is turned into an accusatory event, a one-sided event against the state of Israel," said Thomas Steg, a spokesman for German Chancellor Angela Merkel.
Iranian President Mahmoud Ahmadinejad, who has repeatedly called for the destruction of Israel and denied the Holocaust, plans to speak as the conference opens.
However, Nobel Peace laureate Elie Wiesel is among the many prominent defenders of Israel who will be present.