The German government has a list of at least 437 flights suspected of being operated by the CIA in German airspace, according to a German magazine.
The report said CIA planes had used the US airbase in Ramstein
The weekly Der Spiegel said two planes alone accounted for 137 and 146 uses of airspace or landings in 2002 and 2003.
"Such planes could be used to transfer presumed terrorists and place them in secret locations," Der Spiegel said.
The issue is likely to be raised when US Secretary of State Condoleezza Rice visits Germany on Monday.
Ms Rice said earlier this week she would provide an answer to a EU letter expressing concern over reports last month alleging that the US intelligence agency was using secret jails - particularly in eastern Europe.
A US rights group, the American Civil Liberties Union, said it was taking the CIA to court over what it said was the violation of both US and international law.
The highly secretive process is known as "extraordinary rendition" whereby intelligence agencies move and interrogate terrorism suspects outside the US, where they have no American legal protection.
Some individuals have claimed they were flown by the CIA to countries like Syria and Egypt, where they were tortured.
The list of suspected CIA flights was handed over by German air traffic controllers at the request of the Left Party, Der Spiegel said in its latest edition to be published on Monday.
It said the aircraft had made landings in Berlin, Frankfurt and the US airbase at Ramstein.
However, the list has not shed any light on what the planes were carrying, the BBC's Tristana Moore in Berlin reports.
A German government spokesman said the list revealed only "how many times which planes of which companies flew in German airspace or landed at German airports".
The timing of the report is unfortunate for Ms Rice, as the issue is likely to be raised directly during her talks with new German Chancellor Angela Merkel next week, our correspondent says.
German Foreign Minister Frank-Walter Steinmeier had already expressed concerns about the reports of CIA flights during his meeting with US officials in Washington last week.