Deputy minister Vesna Mikic comes from Kosovo's Serb minority which accounts for about 5 percent of the country's population of 1.8 million.
"The NATO alliance committed a deliberately planned genocide against a sovereign country that fought Albanian terrorism inside its own borders," Mikic said on her Facebook account on Sunday, marking the 20th anniversary of the NATO bombing.
NATO carried out air strikes in 1999 against the now defunct Yugoslavia, comprised of Serbia and Montenegro, to halt a brutal crackdown against Kosovo Albanians by Serbian security forces, Presstv Reported.
After 78 days of bombing, under the terms of an armistice, former Yugoslav President Slobodan Milosevic ordered his troops to withdraw from Kosovo and be replaced with NATO control.
Mikic's post sparked criticism in the predominantly ethnic Albanian Kosovo where most people praise NATO for halting the two-year war and clearing the way for its independence in 2008. As many as 4,000 NATO peacekeepers are still deployed.
Mikic was not immediately available for comment.
Haradinaj dismissed the deputy minister with immediate effect.
"In Kosovo government there will be no place for individuals, despite their ethnicity, to denigrate our common euro-Atlantic values," Haradinaj said in a statement.
More than 13,000 thousand people, mainly local Albanians, were killed in the 1998-99 war.
Kosovo has earned recognition from the United States and most EU countries, but Serbia and its major allies Russia and China remain adamantly opposed to Kosovo's independence.