Top officials in both countries knew of the detention centers, according to the report by Swiss Senator Dick Marty, a former prosecutor who investigated on behalf of the Council of Europe.
The council, a human rights watchdog for several European nations, called for the investigation after media reports of secret CIA prisons emerged in 2005.
Marty did not rule out the CIA having more such prisons in Europe, but told reporters he did not include that in his report because his sourcing was insufficient. He accused Germany and Italy of obstructing investigations into secret detentions.
The report said its conclusions about the clandestine prisons relied on "multiple sources which validate and corroborate one another." Marty said his team spoke with "over 30 one-time members of intelligence services in the United States and Europe" as well as former or current detainees and human rights activists.
While conceding at a news conference that sources for the report were limited, Marty said they were "well placed," including some who "were implicated."
The alleged prisons were at the center of a "spider's web" of purported human rights abuses that Marty outlined in his initial investigation a year ago.
That report focused on flights to spirit detainees to CIA hideouts with landing points in at least 14 nations.
Clandestine prisons and secret CIA flights involving European countries would breach the continent's human rights treaties, although the Council of Europe has no power to punish countries. The council, which is separate from the European Union, was set up four years after World War II to promote democracy, human rights, and the rule of law in Europe.
Officials at the EU have said previously that they trust the denials of Poland and Romania about hosting secret jails.
CIA spokesman Paul Gimigliano did not address whether there were secret detention centers, but he disputed the report's characterization of the agency's activities.
"When you see words like apartheid and torture in the document, that tells you it's biased and distorted," he said. "The CIA's counterterror operations have been lawful, effective, closely reviewed, and of benefit to many people -- including Europeans -- in disrupting plots and saving lives. Our counterterror partnerships in Europe are very strong."
Bush acknowledged the existence of a secret detention program last September, when he announced the CIA had moved Sheikh Mohammed and 13 other suspected terrorists to the US prison at Guantanamo Bay.
