"Just as we have called on believers to pray and fast for a just verdict, we now appeal to Croatian citizens to be calm and dignified," reads a statement issued by the commission.
The Hague-based UN tribunal is to deliver the verdict in the case of the three generals on Friday.
In its statement the commission cites problems which it says the Hague tribunal has failed to deal with appropriately.
"The Hague tribunal has not assessed in a proper way the fact that Croatia was a victim of the Serb aggression," reads the statement.
Iustitia et Pax believes that the court has laid down criteria which are partial and selective rather than universal.
"Thus it has happened that in the 21st century, under the auspices of the United Nations' Security Council, we have an institution in which the big try the small according to criteria not applied to the big," the bishops warn.
The commission says that the UN Security Council and the European Union adopt important political decisions on Croatia based on reports by the Hague tribunal's prosecutor and not on reports compiled by the ICTY president or the tribunal's trial chambers.
The statement also recalls mistakes made by the Croatian side, such as selective and unlawful providing of documents to the ICTY prosecution, notably the so-called "presidential" transcripts.
Iustitia et Pax says that in making its ruling the Hague tribunal should take into account the fact that Croatia had the right and obligation to liberate its occupied areas.
One cannot deny that individual crimes were committed by Croatians, but the actual perpetrators of those crimes should be prosecuted and brought to justice rather than choosing suspects "according to the political key," reads the statement.