Ms Del Ponte provoked anger in Rome and Zagreb when she said that Ante Gotovina, a former general indicted for war crimes, is hiding in a monastery in Croatia.
Her comments come at a sensitive time, since Croatia's bid to start EU membership talks will be re-examined in the next few weeks. Zagreb's ambitions have been put on hold until the authorities there are deemed to be giving full co-operation to the UN's war crimes tribunal.
While Ms Del Ponte highlighted the responsibility of the Church, rather than the state, for shielding Mr Gotovina, her comments also contradict the Croatian government's claims that the general is not on its soil.
Instead Ms Del Ponte told The Daily Telegraph she has information that he "is hiding in a Franciscan monastery and so the Catholic Church is protecting him. I have taken this up with the Vatican and the Vatican refuses totally to co-operate with us."
She added that the Vatican could probably pinpoint exactly which of Croatia's 80 monasteries was sheltering him "in a few days".
A Vatican spokesman, Joaquin Navarro-Valls, said Archbishop Giovanni Lajolo, the Vatican's foreign minister, asked Ms Del Ponte for evidence of Mr Gotovina's whereabouts, but that she never provided more information. He added that the chief prosecutor was trying, improperly, to use the Vatican as an enforcement tool.
Anton Suljic, spokesman for the Croatian Bishops' Conference, said the leadership of the Catholic Church in Croatia "has no information whatsoever or indications concerning the whereabouts of the runaway general Gotovina".
The Croatian Prime Minister, Ivo Sanader, reiterated his insistence that "based on all the information we're getting, Gotovina is not in Croatia".
But Ms Del Ponte's spokeswoman, Florence Hartmann, said: "We are asking for full co-operation from every segment of society: the Church, the military, the politicians. Every segment of society is obliged to respect the law. No one is above the law and we are asking for co-operation from everyone." General Gotovina is alleged to have arranged the killing of at least 150 Serb civilians and the expulsion of 150,000 others during an operation against the Krajina Serbs in 1995. But many in Croatia regard him as a hero.
Meanwhile, fears that nationalists had begun a terrorist campaign to destabilise Zagreb's EU membership bid were calmed yesterday when Croatian police arrested a man suspected of causing a blast at the British embassy in Zagreb on Monday.
The Internal Affairs Minister, Damir Kirin, said the suspect, Damir Rovisan, 28, was a local employee and that the device exploded as he tried to smuggle it into the embassy via the mail room. He said it was a "criminal" act, rather than an act of "terrorism".