The head of the Serbian Orthodox Church was speaking at a service for the Serb victims of the 1990s wars.
He said that by acquitting the Croatian generals, the tribunal had compromised law and justice, confirming that it was not founded on legal norms but the interests of power-wielders.
He said that "in the Hague tribunal's logic, nobody is accountable for 200,000 displaced persons, for burned down Serb homes... and thousands of people killed."
"The Hague tribunal is evidently covering up the crimes against Serbs," Patriarch Irinej said at the service attended by Prime Minister Ivica Dacic, Deputy PM Aleksandar Vucic, Parliament Speaker Nebojsa Stefanovic, ministers, MPs and representatives of state institutions.
The religious head also said that "Serbia respects Europe and wants to be with it but not at the cost of renouncing its holy land" Kosovo, Belgrade's media reported.
He urged the state leadership to establish the closest possible ties with Russia.
After the service, a protest procession headed towards the Serbian parliament. It was organised by the Coalition of Refugees and Displaced Persons whose president, Miodrag Linta, presented Stefanovic with a request for a special parliament session and a draft resolution on respect for the human rights of refugees, the displaced and other damaged citizens from former Yugoslav republics.
The aim of the resolution is for the Serbian government to commit to opening dialogue with Zagreb and Belgrade on the settlement of property and other issues.