In her book called The Hunt: Me and War Criminals, Carla del Ponte described atrocities against Kosovo Serbs and other ethnic groups committed by the Kosovo Liberation Army (KLA).
"Batching freedom of speech concerning crimes against civilians, one may assume, is aimed at softening the reaction within international social and political circles to the facts revealing the criminal prehistory to the illegitimate sovereignty of Kosovo," the ministry said.
On Monday, the ministry denounced a ruling by the International Criminal Tribunal for the Former Yugoslavia last week which saw a former Kosovo prime minister acquitted for crimes committed during the conflict between Kosovo and Serbia in 1998-1999.
Ramush Haradinaj, 39, a former KLA guerilla leader, accused of organizing the rape, murder and intimidation of thousands of Serbs and Roma was found 'not guilty' on April 3.
The ministry said in an official statement the verdict "questions the impartibility and objectiveness of the International Criminal Tribunal" and accused the court of "double standards" in their treatment of conflicts in the former Yugoslavia.
According to claims made in del Ponte's book, Haradinaj was involved in the sale of organs, taken from prisoners executed in Kosovo.
She alleges that there was sufficient evidence for prosecution of Kosovo Albanians involved in war crimes, but it "was nipped in the bud" focusing on "the crimes committed by Serbia."
The claims have caused a storm in Serbia and among the international community. The president of the Association of Families of Kidnapped and Missing Serbs in Kosovo, Simo Spasic, said he wanted to sue Carla del Ponte for "concealing the crimes."