Some human rights experts say US abuses at Abu Ghraib prison in Iraq and its treatment of detainees at the Guantanamo Bay prison in Cuba, may have made it hard for Washington to win election to the council.
Kenneth Roth, executive director of Human Rights Watch, said it was "childish" for Washington not to run for a seat, even though it risked the embarrassment of possible failure.
"It's unfortunate that the Bush administration's disturbing human rights record means that the United States would hardly have been a shoo-in for election to the council.
"Today's decision not to run seems like an effort to make a virtue of necessity," he said.
State Department spokesman Sean McCormack explained Thursday's decision this way: Many democracies with strong human rights records had already put themselves forward for the May 9 election and "it's only fair that they have the opportunity to run for a seat on a council for which they have voted".
The US would probably seek a seat on the 47-member council next year, but would meanwhile support the council financially and encourage it to address human rights abuses in Iran, Cuba, Zimbabwe, Myanmar, Sudan and North Korea, McCormack added.
At UN headquarters, UN chief spokesman Stephane Dujarric said Kofi Annan, the secretary-general, was disappointed but hoped Washington would run for a seat next year.
The decision drew mixed reactions from the US Congress.
Tom Lantos, the senior Democrat on the House of Representatives international relations committee, called the decision "a major retrenchment in America's long struggle to advance the cause of human rights around the world".
"It's unfortunate that the Bush administration's disturbing human rights record means that the United States would hardly have been a shoo-in for election to the council. Today's decision not to run seems like an effort to make a virtue of necessity"
Kenneth Roth, executive director of Human Rights Watch
"It is a profound signal of US isolation at a time when we need to work co-operatively with our Security Council partners," he said.
But Bill Frist, the Senate majority leader who is considering running for his party's 2008 presidential nomination, praised the decision.
He said the US president had made a courageous decision that would deny the rights council unwarranted legitimacy.
He urged George Bush to establish a council of democracies outside the UN system that could meet regularly to monitor and expose human rights abuses around the world.
The 191-member UN General Assembly voted overwhelmingly on March 15 to create the new human rights body to replace the discredited UN Human Rights Commission, whose current members include Zimbabwe, Sudan, Cuba and Saudi Arabia, all of whom have poor rights records.
So far 35 nations have submitted their candidacies for three-year terms, including Cuba and Iran as well as US allies Canada, Britain, Germany and France.
Council members must be elected by an absolute majority of the 191 UN states, as compared to the former practice of voting for regional slates.