During Friday's news conference he held in Ljubljana together with his guest, Cypriot Foreign Minister Giorgos Lilikas, the Slovene official responded to questions about the ongoing dispute between Croatia and Italy on events in the 1930s and 1940s.
Rupel said that Ljubljana did not enter into the discussions between Croatian and Italian Presidents Stjepan Mesic and Giorgio Napolitano about the causes of the tragedy of Italians from the eastern coast of the Adriatic Sea towards the end of the Second World War.
He added that he had sent a letter to Italian Foreign Minister Massimo D'Alema urging Rome to officially confirm the report of the above-mentioned commission.
The report was prepared by a group of Italian and Slovene historians while Slovenia had the status of European Union acceding country.
The document finalised in 2001 contains figures and data about the periods of Fascism, the Second World War and the Communist rule in the wake of WW2.
"In the letter I have suggested to my colleague D'Alema that it might be good for the Italian side to officially confirm the report," Rupel said, adding that it might reflect the fashion in which both sides treat historical issues.
In Slovenia, the report was made public in 2001, while Italy has yet neither presented it officially nor verified it.
Recently, Italian President Giorgio Napolitano ascribed the responsibility for Italian victims at the end of the Second World War in the former Yugoslavia to "Slavic bloodthirsty hatred" and "aspirations for annexation". It was Croatian President Stjepan Mesic to be the first to respond to this language, saying on Monday that the speech contained traces of overt racism, historical revisionism and political revenge-seeking.
Slovene scholars and academicians also called on the governments to respect the historical truth and in this context recalled the joint commission's findings. The Slovene Academy of Arts and Sciences expressed concern over the "distorted" presentation of the topic in the Italian media and over Napolitano's speech.
Two Slovene deputies in the European Parliament, Mojca Drcar Murko and Jelko Kacin, on Friday condemned the Italian leader's speech portraying it as an attempt to deny the 1947 Paris peace treaty that defined the border between Italy and the then Yugoslav Federation.
The members of the European Parliament believe that the Slovene Government should have responded to such language.
"Napolitano's speech negates the Paris Peace Treaty and this is a European problem," Mojca Drcar Murko said.
Kacin said the issue certainly concerned Slovenia which was why Ljubljana should take a clear position on the matter.
Kacin added that the time had come for Slovenia to show solidarity with Croatia and that Slovenia should have backed Zagreb during the latest diplomatic dispute.
The two MEPs announced an initiative in the European Parliament aimed at condemning a recent arson attack against the kindergarten for Slovene children in Trieste.
Another Slovene deputy in the European Parliament, Borut Pahor, said that he was hurt and saddened by Napolitano's speech.
He described the speech as "an unacceptable and distorted way of shedding light on some events from the recent past".
Pahor also called on the Slovene Government to respond to Napolitano's language.
It is necessary to speak about the truth, the whole truth, no matter how painful it can be, Pahor said today.
Before 1943, the Italian regime led by Benito Mussolini tried to ruthlessly Italianise the Slavic-populated regions of the Adriatic coast which it annexed in the late 1930s.
After Mussolini's capitulation in 1943, Yugoslav Partisans led by Josip Broz Tito liberated those areas and disputed border regions. In that period thousands of Italians were forced to leave their homes on Slovenia's and Croatia's coast.
Scholars estimate that several thousand people, mainly Italians, were executed and many of them were thrown in the karst pits known as foibe.
Two years ago, Italy introduced a memorial day on 10 February commemorating foibe victims.