In April 1999, during the NATO bombing of Yugoslavia, Kurti was arrested and beaten by Yugoslav forces. He was first sent to the Dubrava prison, but as the Serbian army withdrew from Kosovo, they transferred him to a prison in Požarevac on 10 June 1999. Later that year, he was charged with "jeopardizing Yugoslavia's territorial integrity and conspiring to commit an enemy activity linked to terrorism" and was sentenced to 15 years in prison.