Carlo Giovanardi, minister for relations with parliament, made the statement in an address to the Senate on Thursday. He was responding to opposition questions about whether Italian authorities knew in advance of plans to kidnap the Egyptian.
Giovanardi said Premier Silvio Berlusconi's government had summoned the US ambassador, who was expected to meet with Italian officials on Friday.
Giovanardi said the reported operation was never "brought to the attention of the government of the republic or national institutions", often a term used to refer to Italy's intelligence agencies.
Therefore, he said, "it is not even possible that any operation of this type was ever authorised".
The prosecution has said it is preparing extradition requests for the 13 CIA operatives, who are accused of seizing Egyptian Osama Moustafa Hassan Nasr, known as Abu Omar, in February 2003.
Prosecutors have asked Interpol help in tracing the suspects, all identified as US citizens.
The abduction was purportedly part of a US government programme called "extraordinary rendition", in which terror suspects are transferred to third countries without court approval, subjecting them to possible torture.
The CIA's powers have greatly
expanded on Bush's watch
Nasr told his wife in an intercepted cellphone call from Egypt that he was tortured, the Milan prosecutor's office has said.
He reportedly was hung upside down and subjected to extreme temperatures and loud noise that damaged his hearing.
The US Embassy in Rome, the CIA in Washington and Egyptian officials have declined to comment.
The Milan prosecutor's office called the imam's disappearance a blow to Italy's own fight against terrorism. He had been under investigation for alleged terrorist activity in Italy at the time of his disappearance.
Responding to Giovanardi, opposition Senator Tana De Zulueta referred to an article in the Washington Post on Thursday that claimed the CIA station chief in Rome had briefed and sought approval from an Italian official before the purported operation, citing three unnamed CIA veterans said to have had knowledge of the operation and a fourth said to have reviewed it after it took place.
One of the veterans claimed in the report that the CIA "told a tiny number of people" about the action. The report said it was unclear how high in the Italian intelligence service the information was shared or whether Berlusconi was made aware.
Opposition parties want to know
what officials knew in advance
At De Zulueta's reference to the article, Giovanardi shouted out: "It's false."
Repeating his address later on Thursday in the Chamber of Deputies, Italy's lower house, Giovanardi called the Washington Post article "a report without any foundation, a false report, which the Italian government is able to deny with great calm".
The 13 alleged CIA officers have been listed by name in a judge's report explaining the need for their arrest, though some of the names might be aliases, as is often a practice of such operatives overseas.
Several gave US post office boxes as their addresses.
One suspect described as playing a key role was identified as former Milan CIA station chief Robert Seldon Lady, 51.
The order said he had been listed as a diplomat, but was retired and living near Turin.
The report said the cellphone records show Lady was in Egypt from 22 February to 15 March, which were likely the first days Nasr was being tortured during interrogations.
It also describes how investigators traced the purported officers through a trail of credit card information and US addresses they gave to five-star hotels in Milan around the time of Nasr's alleged abduction, as well as their use of Italian cellphones.