The trial will be the biggest ever of US intelligence agents in an allied country, although they will almost certainly be tried in absentia.
The Italian government has not yet sought the US citizens' extradition.
Bob Seldon Lady, the former CIA station chief in Milan and one of the defendants, said via his lawyer last month that he did not recognise the court.
"I have been reduced to a wreck of a human being"
All of the US agents have court-appointed lawyers, who have said they have had no contact with their clients.
Alessia Sorgato, a lawyer who represents three Americans, said she was happy about the ruling because she would be able to fully argue the case in court.
Judge Caterina Interlandi ordered the trial to start on June 8.
An Italian policeman, Luciano Pironi, has recieved a 21-month prison sentence as part of a plea-bargain deal after admitting stopping Omar on the street so the CIA could grab him.
He says the CIA told him they were trying to recruit Omar and that the operation was approved by Rome and the US.
Pollari says Italian military intelligence did nothing wrong but has not co-operated with the court, saying the evidence is covered by the state secrets act.
Omar said he was snatched from a Milan street and bundled into a van.
The cleric is thought to have been taken to the US air base in Aviano, northern Italy and from there transported to Egypt.
Omar was released from prison on Sunday and says he would like to return to Italy.
"I have been reduced to a wreck of a human being," he told ANSA news agency after his release.
The European Parliament approved a report on Wednesday that said governments in the region helped conceal secret US transfers of terrorism suspects.
And prosecutors elsewhere in Europe are going ahead with cases aimed at the transfers.
This week, the Swiss government approved prosecutors' plans to investigate the flight that allegedly took Omar over Swiss air space from Italy to Germany.
And a Munich prosecutor recently issued arrest warrants for 13 people in connection with another alleged CIA-orchestrated kidnapping - a German citizen who says he was abducted in December 2003 at the Serbian-Macedonia border and flown to Afghanistan.