Milutin Graic, 41, is accused of being a member of a militia that ethnically cleansed Croats, deporting them from the self-proclaimed statelet of Serbian Krajina, which was carved out of the territory of newly independent Croatia in the early 1990s.
Prosecutors said a Croatian court had issued a European arrest warrant for the man, who had been living on the run in the southern city of Roosendaal, near the Netherlands' border with Belgium.
His extradition is likely to follow soon. The Croatian Justice Ministry had no immediate comment. The Balkan wars of the 1990s followed the break-up of multi-ethnic Yugoslavia.
Which cost more than 100,000 lives as successor states Serbia and Croatia sought to carve ethnically pure states out of each others' territories and on the territory of multi-ethnic Bosnia.