The Swedish defence forces conducted a secret surveillance operation in 2005 monitoring a US government plane at Stockholm Arlanda Airport.
"The assignment to carry out this operation came from the defence ministry to the defence forces," according to an Expressen source who confirmed that the Swedish government harboured suspicions that the CIA was using so-called rendition flights to force people out of the USA against their will.
The surveillance team confirmed these suspicions and found that the CIA plane was filled with chained prisoners clad with black hoods and unable to move, the newspaper reports, citing several independent anonymous sources.
The Swedish defence forces on Friday confirmed to the newspaper that the surveillance operation took place.
"We have inspected the plane but make no further comment," Roger Magnergård, press officer at the Swedish defence forces, said to Expressen.
The operation's findings were reported back to the defence department, then headed by defence minister Leni Björklund, Expressen writes.
There is however no record of any formal protest lodged by the Swedish government to the US authorities.
Laila Freivalds, the Swedish foreign minister at the time, told the TT news agency in 2006 that the government was unaware of any CIA-backed activity in Sweden.
The only other known case of a CIA plane that used Sweden as a transit country emerged in 2004 and concerned two Egyptian asylum-seekers who were collected at Bromma airport in 2001 and flown to Egypt.
Ahmed Agiza and Mohammed Alzery, it later emerged, were then subjected to torture and were in 2008 each awarded 3 million kronor ($363,765) in compensation by the Swedish government.