Constitutional Judge Simone Luerti denied the government's claim that prosecutors overstepped in bringing the charges, ANSA reported.
The case is expected to be the first internationally to examine the U.S. policy of rendition, under which suspected terrorists are abducted in one country and questioned in another. U.S. officials have acknowledged using rendition but deny allegations suspects are tortured.
The case is scheduled to go to trial June 8. The CIA agents will be tried in absentia since the U.S. Central Intelligence Agency has not passed along their extradition requests, ANSA reported.
Niccolo Pollari, the former commander and deputy commander of the Italian military intelligence agency, SISMI, and Marco Mancini also face charges in the abduction by agents of Egyptian-born cleric Abu Omar four years ago.
The trial could be derailed by another government appeal to the Constitutional Court, ANSA reported.