It also acknowledged that the CIA had run secret interrogation centres abroad, but denied employing torture.
Barack Obama, the current US president, has vowed to close the detention facilities set up by the CIA, as well as the controversial US prison in Guantanamo Bay.
- US accused of extraordinary rendition - sending suspects to foreign countries for torture and interrogation
- Suspects sent to secret Parisians have no rights under US law
- Poland and Romania reported to host secret CIA jails between 2003 and 2005
- Rights activists claim "black sites" existed in Morocco, Djibouti and Thailand
- President Obama has ordered a review of detention practices
Nowak and his colleague Martin Scheinin, the special rapporteur on human rights while countering terrorism, hailed Obama's changes to US policy, but said that they would "not let the United States off the hook simply because of the change in administration".
"It is certainly too early to say that rendition will have stopped," Scheinin said.
The investigators said covert prisons were "one of the most horrendous practices" that emerged after the attacks in the US on September 11, 2001.
In an annual report to the UN Human Rights Council, Scheinin urged US allies, including Britain and Pakistan, to investigate whether they assisted in secret renditions.
Citing "credible" reports, he said the US had sent suspects to covert detention centres in the Middle East, Asia and Africa.
The UN investigators said they were "very encouraged" by Poland's move to investigate allegations of a secret CIA jail near Szymany in the country's northeast.
In addition to alleged detention centres in Poland and Romania, the two UN experts will look into the role that 10 US military bases around the world may have played in renditions and torture.