The charge follows a separate investigation by the European Union into claims that the CIA secretly held suspects in Europe and flew some to states that carry out torture, a practice known as extraordinary rendition.
On Wednesday, the European Parliament passed a resolution saying it "condemns extraordinary rendition as an illegal instrument used by the United States in the fight against terrorism".
In testimony obtained by Reuters, Gianfranco Battelli, head of Italian military intelligence agency SISMI in 2001, told prosecutors: "[The CIA station chief in Rome] asked my opinion, 'What do you think' about the hypothesis of carrying out the strategy of so-called renditions".
The deposition of Battelli, who stepped down long before the abduction and is not a defendant, says the CIA official "made explicit reference to the possibility of grabbing a terrorist suspect in Italy, taking him to an airport and from there boarding him to a foreign country".
If the judge, Caterina Interlandi, orders a trial it would be the world's first criminal case over renditions, one of the most controversial aspects of George Bush's so-called "war on terror".
Hassan Mustafa Osama Nasr, also known as Abu Omar, says he grabbed off a Milan street, driven to a US military base in northern Italy and flown to Egypt, where he alleges he was tortured under interrogation.
The Italians linked to the Nasr case have been defending themselves tooth-and-nail, in the process making compromising statements about their US counterparts and each other.
All claim to have personally refused to help the CIA in the kidnap itself, except an Italian police officer who says he was told by the CIA's Milan station chief that the purpose was to recruit the cleric as an informer, not to abduct him.
A court in Munich issued arrest warrants last month for 13 suspected CIA agents accused of kidnapping a German of Lebanese descent and flying him to an Afghanistan jail, where he too says he was tortured.
Battelli said he told the CIA chief he was on his way out of office and that the CIA should talk with his successor Nicolo Pollari.
Pollari is the highest-level Italian official facing indictment and denies any wrongdoing.
He has complained that evidence proving his innocence is being kept classified by Romano Prodi, Italy's prime minister.
Prodi, who took office in May, said the files were classified by his predecessor, Silvio Berlusconi.
Nasr was released from an Egyptian prison on Sunday four years after his suspected rendition.
He says he was tortured with electric shocks, beatings, rape threats and genital abuse.
He told Italy's Ansa news agency: "I've been reduced to a wreck of a human being."