THE HAGUE, Sept 15 (Reuters) - A special tribunal in The Hague investigating allegations of atrocities committed by Kosovo pro-independence fighters opened its first case on Wednesday, against a commander accused of torturing prisoners during the 1998-1999 conflict with Serbia. At the start of his trial, Salih Mustafa, 50, pleaded not guilty to charges of war crimes, comparing the court to the Nazi secret police. "I am not guilty of any of the counts brought here before me by this Gestapo office," Mustafa told judges. The Kosovo Specialist Chambers, a Kosovo court seated in the Netherlands and staffed by international judges and lawyers, was set up in 2015 to handle cases under Kosovo law against fighters of the Kosovo Liberation Army (KLA). It is separate from a U.N. tribunal, which was also located in The Hague and tried Serbian officials for crimes committed in the same conflict. The Kosovo tribunal"s highest-profile suspect is former Kosovo President Hashim Thaci, who turned himself in last year to face charges of war crimes and crimes against humanity. In the court"s first case, Mustafa faces charges of murder, accused of running a prison unit where inmates where subjected to daily beatings and torture. Prosecutors explained that in Mustafa"s case his victims were also Kosovo Albanians. "Certain leaders of the KLA, including mister Mustafa, used their power to victimize and brutalize fellow Kosovo Albanians including individuals whose only crime was to have political views that differed from those of the KLA and its leaders," prosecutor Jack Smith said. Mustafa"s indictment says he personally took part in some of the beatings and torture of at least six prisoners and was present when an inmate was so badly hurt that he later died.After listening to the prosecution opening statement Mustafa, dressed in red and black athletic gear and occasionally fidgeting with a pen, did not return to court to hear the opening statement of lawyers for the victims. The judges allowed Mustafa to be absent from proceedings for the rest of the day, adding that his interests would be represented by his lawyer. More than 13,000 people are believed to have died during the 1998-99 war in Kosovo, when the southern province was still part of Serbia under the rule of late Yugoslav President Slobodan Milosevic. Fighting ended after NATO air strikes against Milosevic"s forces, and Kosovo is now an independent country. KLA fighters are considered heroes by many in Kosovo, and opponents of the tribunal consider it unfair that they are being prosecuted, arguing that Serbia has undergone no analogous effort to bring its own commanders to justice.