The CIA operated secret prisons in Europe where terrorism suspects could be interrogated and were allegedly tortured, an official inquiry will conclude tomorrow.

Despite denials by their governments, senior security officials in Poland and Romania have confirmed to investigators for the Council of Europe that their countries were used to hold some of America's most important prisoners captured after 9/11 in secret.

None of the prisoners had access to the Red Cross and many were subject to what George Bush has called the CIA's "enhanced" interrogation methods. These included water-boarding which leads detainees to believe they are drowning, which critics have condemned as severe torture.

Although suspicions about the secret CIA prisons have existed for more than a year, the council's report, which has been seen by the Guardian, appears to offer the first concrete evidence. It also details the prisons' operations and the identities of some of the prisoners.

The council has also established that within weeks of the 9/11 attacks, Nato signed an agreement with the US that allowed civilian jets used by the CIA during its so-called extraordinary rendition programme to move across member states' airspace.

The report states: "We have sufficient grounds to declare that the highest state authorities were aware of the CIA's illegal activities on their territories."

That agreement may have been illegal, the council's investigators believe.

The full extent of British logistic support for the extraordinary rendition programme was first disclosed by the Guardian, which reported in September 2005 that aircraft operated by the CIA had flown in and out of UK civilian and military airports hundreds of times.

The 19-month inquiry by the council, which is responsible for promoting human rights across Europe, was headed by Dick Marty, a Swiss senator and former state prosecutor. He said: "What was previously just a set of allegations is now proven: large numbers of people have been abducted from various locations across the world and transferred to countries where they have been persecuted and where it is known that torture is common practice."

His report says that there is "now enough evidence to state that secret detention facilities run by the CIA did exist in Europe from 2003 to 2005, in particular in Poland and Romania".

Mr Marty has told Channel 4's Dispatches, in a report to be broadcast on Monday, that although the jails were run "directly and exclusively" by the CIA with local officials barred from access the prisons were only possible because of "collaboration at various institutional levels of America's many partner countries".

He succeeded in confirming details of the CIA's closely-guarded secret by using his own "intelligence methods", which included tracking and persuading to talk intelligence agents on both sides of the Atlantic, including serving members of the CIA's counter-terrorism centre.

"All the conclusions drawn in this report rely upon multiple sources," he said.

He concludes that in eastern Europe, the CIA had trusted "point-men" who alone knew about the prisons; their partners were Poland and Romania's military intelligence agencies who reported directly to then president Aleksander Kwasniewski in Poland, presidents Ion Iliescu and then Traian Basescu in Romania, and their nearest security advisers.

This meant that civilian intelligence agencies, parliamentary oversight committees, and even the countries' prime ministers could "credibly deny" knowledge of the CIA facilities.

In Poland the main CIA jail was in a former Soviet-era military compound at Stare Kjekuty, near Szmany airport in north-eastern Poland. This prison was for the most high value detainees, known as HVDs. Those held there included Khalid Shaikh Mohammed, the alleged architect of 9/11.

It was at the Polish site, said Mr Marty, that some of the CIA's "enhanced methods" of interrogation, such as extreme sleep deprivation and water-boarding were used. "These methods amounted to illegal torture," he told Dispatches.

Mr Marty concludes that the CIA was able to move around Europe, flying prisoners to its secret sites and organising renditions of prisoners to other countries, due to an agreement signed by all Nato members, including Britain, just after September 11.

On October 4 2001, Nato's then secretary-general, Lord Robertson, had said alliance members had agreed to grant "blanket over-flight clearances" as well as basing rights to US forces involved in the so-called war on terror. Although Lord Robertson referred only to military flights, the full text of the agreement has remained classified.

Quoting its own confidential sources, the Council of Europe says a secret part of the agreement also gave total freedom of movement for the civilian jets used by the CIA for its prisoner operations.

Government officials in Poland and Romania have repeatedly denied the existence of CIA facilities or the presence of detainees held by US authorities.

But Mr Marty concluded: "All the members and partners of Nato signed up to the same permissive - not to say illegal - terms that allowed CIA operations to permeate throughout the European continent and beyond; all knew that CIA practices for the detention, transfer and treatment of terrorist suspects left open considerable scope for abuses and unlawful measures; yet all remained silent and kept the operations, the practices, their agreements and their participation secret."

There was no immediate comment from Nato.

· Stephen Grey presents Dispatches - Kidnapped to Order on Monday June 11 at 8pm on Channel 4