Poland will clear its former intelligence head of charges he knew about and permitted the CIA to run a secret prison on Polish soil to detain and torture Al-Qaeda suspects, according to a local newspaper.

Gazeta Wyborcza cited a source revealing that charges against former intelligence chief Zbigniew Siemiatkowski will be dropped.

"The decision ... has been taken by Krakow-based prosecutors," the newspaper said on Tuesday.

The Polish prosecution declined to comment.

Official criminal investigation into CIA-run secret prison in Poland began in 2008 and Siemiatkowski became implicated in early 2012 after allegations about how much he really knew about the prison came to light.

The government has refused to say whether the Siemiatkowski was ever officially charged or not. But according to sources close to the investigation, charges were drawn up against him in 2012, Reuters reported.

Lawyers and activists argued in January that the investigation was being suppressed because it would embarrass the top echelon of the country’s government. Linking them with illegal detention and torture, it would also impact negatively on the relationship between Poland and its key ally, the US.

Siemiatkowski was the head of Polish domestic civilian intelligence agency during the time the ‘black sites’ were allegedly functioning. In 2005 he left office.

The investigation took on a twist when the original investigators were taken off the case in early 2012 and the case was transferred from the capital, Warsaw, to the southern city of Krakow.

"All these decisions are so irrational from the point of view of the effectiveness of the investigation [that] it is realistic to assume there is some political interference," vice-president of the Warsaw-based Helsinki Foundation for Human Rights Adam Bodnar told Reuters.

Beginning in 2005, former CIA officials and activist groups began to reveal more information about the CIA-run prison in Poland.

It was said to be in a small remote village Stare Kiejkuty and was operational from December 2002 to the fall of 2003. It was used to transport suspected Al-Qaeda members outside the US territory to interrogate without having to adhere to US law.

A report released by the Open Society Justice Initiative (OSJI), a New York-based human rights organization, argued that at least 54 countries including Poland, Syria, Iran, Sweden, Iceland, and UK offered the CIA ‘covert support’ to detain, transport, interrogate and torture suspects in the years following the 9/11 attacks.

Poland is said to have “hosted a secret CIA prison on its territory, assisted with the transfer of secretly detained individuals in and out of Poland, including to other secret detention sites, and permitted the use of its airspace and airports for such transfers,” according to the report.

In 2006, then-President George W. Bush revealed the US had CIA detention facilities overseas, but no details came out as to their exact locations.

The CIA’s black sites in Europe are rumored to have detained and tortured suspected terrorists, and to hold them in custody before being transported to the prison at Guantanamo Bay.

The sites and the prisoners existed in legal limbo, with no oversight from citizens of the host countries. The CIA is believed to have operated with the knowledge and cooperation of the governments of those countries.

Poland has continuously denied that there were operational secret CIA prisons on their territory, but promised to carry out a fair investigation.

It is the second country to have opened a criminal investigation into the matter, after Lithuania (though that case has been closed).

Polish prosecution had requested an extension to the five-year investigation, but the time-frame of that extension remains unknown.