Dinamo Zagreb president Zdravko Mamic has been charged with inciting racial hatred towards Croatian sports minister Zeljko Jovanovic and all ethnic Serbs.
Croatia's state prosecutors, in line with the law, failed to name the Dinamo chief but said that a 54-year-old Croatian committed the crime while appearing on a local radio talk show.
Mamic told the Zagreb-based Soundset Plavi radio that Jovanovic, an ethnic Serb, "hates everything Croatian".
"A Serb should not be in charge of one of the most important sectors in Croatia," Mamic said.
There has been tension between Mamic, a powerful figure in Croatian football, and Jovanovic, a member of the 18-month old Social Democrat-led government, for some time, with the politician publicly calling for an investigation into the irregularities of the sport in Croatia.
Croatia, which will join the European Union on July 1, broke away from communist Yugoslavia in 1991, before waging a war against its ethnic Serb minority who opposed its independence.
The war ended in 1995 but ethnic mistrust between Croats and Serbs still exists.