Prime Minister Silvio Berlusconi on Friday summoned US Ambassador Mel Sembler for a nearly hour-long meeting after accusations the US broke Italian law by seizing the cleric and taking him to Egypt, where prosecutors think he was tortured.
Italy, a US ally in the "war on terrorism" and Iraq, has denied prior knowledge of any kidnapping.
"Berlusconi received ... the United States ambassador, Mel Sembler, to whom he explained the indispensable demand that the United States fully respect Italian sovereignty," the prime minister's office said in a statement.
The US embassy, which has declined to comment on the kidnapping allegations, said Sembler told Berlusconi it was US policy to always respect Italy's sovereignty.
"Both the prime minister and ambassador underscored that the broad, deep and lasting ties between the United States and Italy will continue on the basis of mutual respect," the embassy said.
Prosecutors think Hassan Mustafa Osama Nasr, also known as Abu Omar, was seized in a Milan street on 17 February 2003, and secretly flown to Egypt. They said evidence showed he was tortured by Egyptian authorities during questioning.
A Milan judge has issued arrest warrants for 13 people in connection with the kidnapping of Nasr. Judicial sources say all 13 are linked to the US Central Intelligence Agency.
Italian media reported on Friday prosecutors were seeking arrest orders for an additional six CIA agents.
It was the second time this year that Italy has publicly summoned Sembler.
Agent killed in Iraq
In March, the ambassador was called in after US troops killed Italian intelligence agent Nicola Calipari in Iraq, provoking a national outcry. No disciplinary action was taken against the US soldiers.
"They hide the truth about Calipari, they kidnap terrorists or terrorist suspects and then don't even bother to give an explanation," opposition lawmaker Pietro Folena told reporters.
The killing of intelligence official
Calipari provoked an outcry
Opposition politicians asked Berlusconi to address parliament on the kidnapping allegations.
The government appeared slow in responding publicly to news of the arrest orders in the Nasr case, only breaking its silence on Thursday but failing to convince critics.
"Exactly because nobody knew, why then wasn't the ambassador summoned last week, when the judge issued the arrest warrants?" leading Italian newspaper Corriere della Sera said in a front-page editorial column.
A political cartoon on Friday showed a picture of Berlusconi covering his eyes so as not to see a CIA officer next to him, wearing a spy's trademark trench coat and dark glasses.
It was a sign of how much the agents appeared to have bungled the operation, according to Italian reports, leaving a trail of hotel receipts and phone records.
One US intelligence officer, declining to be identified, said it was "beyond appalling".