The video clip titled "Polish Jihad," in which young people in masks are waving axes and machetes and voicing threats to refugees, appeared on YouTube late last year.
"A group of men recorded a clip near the center for refugees, in which they threatened its residents. Three of them face charges of inciting hatred against national and ethnic minorities," the center said in a statement.
Europe has been beset by a refugee crisis, with hundreds of thousands of undocumented migrants fleeing their home countries in the Middle East and North Africa to escape violence and poverty.
Poland is among countries which have opposed the EU quota scheme for refugee redistribution across Europe, approved last September. Under the plan, Poland would have to accept some 7,000 refugees.