The SRS protest took place on Wednesday as Croatia was celebrating, and Serbia observing a day of mourning on the 20th anniversary of Croatia's Operation Storm - a campaign that resulted in a mass expulsion of ethnic Serbs.
Croatian media are reporting that Zagreb delivered the protest note to Serbian embassy's charge d'affairs, Bosa Prodanovic.
Croatian Deputy FM Zeljko Kupresek reiterated it was "impermissible for accused war criminal Vojislav Seselj and a handful of his supporters to, unimpeded by the police, set Croatian flags on fire, and remind with his statements of the 1990's rhetoric."
"We condemn such statements and completely reject them. It is demonstrated once again that the statements of accused war criminals, beside damaging Serbia, also damage regional cooperation, relations between the countries in the region and the European path," he said.
The Croatian official added that the events that preceded the incident "did not contribute to the calming of the situation, to more rational and responsible actions," and that speeches given by top Serbian officials had "a counterproductive effect on the normalization of relations between the countries."
"In this context we consider the statement of Serbian President Tomislav Nikolic that Croatia was, with Storm, celebrating victory and a day when the state inherited from (Ante) Pavelic - recognized only by Hitler - was renewed, as completely inaccurate, offensive, impermissible, and irresponsible," a statement said.