Bleiburg was the site of planned executions of thousands of people, said Seks, under whose auspices the commemoration of the 60th anniversary of the Bleiburg tragedy was held.
He said those innocent victims must be remembered and that the truth about all war victims should be established.
Seks said the criminalisation of Flash and Storm, two 1995 operations which liberated occupied parts of Croatia, would not be allowed, to which many of those in attendance shouted "Ante! Ante", alluding to Ante Gotovina, a fugitive Croatian general wanted by the Hague war crimes tribunal.
In his sermon in memory of all victims, Puljic said, "Stop with the double standards in the honouring of victims!" He added that victims should not be used for the creation of a mythology or an ideology.
Puljic said that every people was entitled to its language, history and culture.
The chief of the Islamic community in Croatia, Sevko Omerbasic, called for forgiveness, while Efendi Aziz Halili prayed for Islamic victims.
Bosnian parliament representative Vinko Zoric said that "the bloody truth from our past should be built into the foundations of our state".
Prior to the mass, Cardinal Puljic consecrated a new monument to the Bleiburg victims, the work of Croatian sculptor Stipe Sikirica.
In May 1945, many Croatian soldiers and civilians started retreating towards the Austrian border to surrender to the Allies. They were stopped at Bleiburg by British troops who handed them over to the Yugoslav partisan army.
According to the Croatian Encyclopaedia's 2000 edition, about 95,000 Croatian soldiers surrendered at Bleiburg. Some prisoners, soldiers and civilians were killed near Dravograd, Maribor and other locations in Slovenia. The encyclopaedia does not specify the number of the victims, saying that various estimates have been given. The majority of those who survived was forced to return to Yugoslavia. Many were killed during death marches, known in Croatia as the Way of the Cross, while many were taken to camps.