John Bellinger, legal adviser at the State Department, said the Bush administration was "absolutely committed to uphold its national and international obligations to eradicate torture".
Lobby groups including Amnesty International and Human Rights Watch, accuse the US of mistreating detainees through cruel interrogation methods including "water-boarding" - a form of mock drowning.
"This committee should not lose sight of the fact that these incidents are not systemic," Bellinger told the committee, which began a two-day investigation of America's record on Friday.
It would be unfair to "focus exclusively on allegations" as "relatively few actual cases of abuse and wrongdoing have occurred in the context of US armed conflict with al-Qaeda", he said.
"I would ask you not to believe every allegation you have heard. Critics will now accept virtually any speculation and rumour circulated as fact," he said.
The US is holding hundreds of al-Qaeda and other suspects, arrested since the September 11 attacks in 2001, at US-run detention facilities in Afghanistan, Iraq and Guantanamo Bay, Cuba.
Scandals involving sexual and physical abuse of detainees held by US forces, including at Abu Ghraib prison near Baghdad, have provoked worldwide outrage.
Last June, Washington acknowledged for the first time to the UN that prisoners have been tortured at detention centres in Guantanamo Bay, as well as Afghanistan and Iraq,
"I would ask you not to believe every allegation you have heard. Critics will now accept virtually any speculation and rumour circulated as fact"
John Bellinger, legal adviser at the State Department
As head of the US delegation to the meeting in Geneva, Bellinger said 30 senior American officials from four agencies would do their best to answer the UN experts' questions fully, but could not comment on intelligence activities.
The UN committee, composed of 10 independent experts, demanded last month that the US provide more information about its treatment of prisoners at home and abroad.
The committee's mission is to keep an eye on respect for the Convention against Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment.
Signatories of the convention have to submit to scrutiny of their implementation of the 1984 convention and to provide information to the committee.
In dozens of questions submitted to Washington, the panel also sought information about secret detention facilities and asked whether the US assumed responsibility for alleged acts of torture in them.
"President Bush has made clear that torture anywhere is an affront to human dignity everywhere," Bellinger said.
Barry Lowenkron, assistant US secretary for democracy, human rights and labour, said: "Torture is wrong no matter where it occurs. The US continues to lead the fight to eliminate it everywhere."
US torture and abuse of detainees - Human Rights Watch