Minister of Local Governance and Administration, Ivan Teodosijevic, was dismissed for comments that expressed "ignorance, hatred and insult" to victims of Kosovo's independence war from Serbia, Haradinaj wrote on Facebook.
Teodosijevic had called the January 1999 killing of 45 Kosovo Albanians in Racak "a fabrication" by "Albanian terrorists who invented everything".
The massacre by Serb forces helped prompt NATO's three-month intervention to halt Belgrade's repression of pro-independent ethnic Albanians in Kosovo, which was then a Serbian province.
While Kosovo and the West concluded the victims in Racak were civilians, many in Serbia believe they were guerilla separatists.
Twenty years after the war, the neighbours still have tense relations, with Belgrade refusing to recognise Kosovo's independence.
Kosovo's ethnic Serb minority also rejects the independence of the breakaway territory, whose constitution requires that Serbs be represented in government.
Belgrade reacted angrily, saying it showed Haradinaj only wants "exclusively loyal Serbs who will give Pristina the image of being multi-ethnic".
Two weeks ago Haradinaj sacked another Kosovo Serb, deputy minister of justice Vesna Mikic, who had said that NATO bombing was "genocide against the Serbian people".
In February he also dismissed Serb Nenad Rikalo from the post of the minister of agriculture.
The 1998-1999 independence war in Kosovo claimed more than 13,000 lives, mostly ethnic Albanians, and led to a humanitarian and refuge crisis with almost one million people fleeing for neighbouring Albania and Macedonia.