Marc Garlasco, an analyst for Human Rights Watch, interviewed in Gazeta Wyborcza, a Polish newspaper, said: "Poland was the main base for CIA interrogations in Europe, while Romania played more of a role in the transfer of detained prisoners."
He said the allegations were based on information from CIA sources and other documents obtained by Human Rights Watch. "We have leads, circumstantial evidence to check but it's too early to reveal them," Garlasco said.
The group said in a statement from its base in New York: "Human Rights Watch has collected information that CIA airplanes travelling from Afghanistan in 2003 and 2004 made direct flights to remote airfields in Poland and Romania.
"Human Rights Watch has not reached conclusions about CIA operations in Eastern Europe. We are continuing to investigate the issue."
Poland and Romania deny hosting secret CIA jails and the US has declined to comment on the reports.
Garlasco was quoted as saying that the CIA had set up two detention centres in Poland, which were closed shortly after the Washington Post published an article about secret prisons last month. The Polish centres held a quarter of the 100 detainees thought to be held in such camps worldwide, he said.
Reports of the CIA operating secret jails in Poland and Romania have caused controversy on both sides of the Atlantic and dogged a European trip this week by Condoleezza Rice, the US secretary of State.
ABC News, the American broadcaster, reported this week that the US held al Qaida suspects at two secret CIA prisons in Eastern Europe until last month, when 11 prisoners were moved to a site somewhere in north Africa.
Polish authorities have repeatedly denied the existence of secret jails on Polish territory.
In a separate development, Marek Nowicki, the UN human rights ombudsman in Kosovo, denied telling a German newspaper that the US had run a secret prison at Camp Bondsteel in the UN-administered Serbian province.
Commenting on a report in the Berliner Zeitung, Nowicki's media adviser said: "In none of (Nowicki's) visits did he see anything that would have indicated that there were such secret prisons at Bondsteel."
But he did confirm Nowicki's view that there was no possibility for any outside body to monitor whether the treatment of prisoners met international human rights standards.
The US military has said that the Bondsteel prison has been closed and no prisoners have been held there since at least February.