Italian Prime Minister Silvio Berlusconi has demanded the US show "full respect" for his country's sovereignty, in an official statement.
Mr Berlusconi stood by the US when an Italian agent was shot in Iraq
His message was delivered to the US ambassador, who was summoned to explain the alleged CIA abduction of an Islamic cleric in Milan in 2003.
Italy denies prior knowledge of the alleged operation to fly Osama Mustafa Hassan, 42, to Egypt for interrogation.
Arrest warrants have been issued for 13 alleged CIA agents.
"The prime minister demanded full respect for Italian sovereignty from the United States," said the statement, which followed Mr Berlusconi's meeting with ambassador Mel Sembler.
The statement said the prime minister received assurances from Mr Sembler that the US' "respect was full and total, and that it would remain so in the future."
Mr Hassan, also known as Abu Omar, was already being investigated in Italy as part of a terrorism inquiry at the time of his reported abduction.
Italian prosecutors believe the operation was part of a controversial US anti-terror policy known as "extraordinary rendition".
The imam was allegedly flown out of Italy from a US military base
The policy involves seizing suspects and taking them to third countries without court approval.
Minister for Parliamentary Relations Carlo Giovanardi has told senators that neither the Italian government nor its intelligence services knew about the operation.
But the Washington Post quoted unnamed CIA veterans saying the CIA station chief in Rome had informed Italian officials in advance.
They said that it was agreed that if the operation became public neither side would confirm its involvement.
No arrests have been made in the case since the warrants were issued. None of the suspects is currently believed to be in Italy.
Mr Hassan, who had been granted refugee status in Italy, was allegedly abducted in February 2003, while walking from his house to his local mosque.
He was then reportedly driven to a US base north of Venice before eventually being taken to Egypt.
The imam told his family he had been tortured with electric shocks during his detention.
Italian investigators say his disappearance hampered an ongoing investigation into alleged terrorist links.
They managed to track down the 13 suspected agents through the Italian mobile phones they used during the operation.