Kubura was first indicted by the International Criminal Tribunal for the former Yugoslavia on 13 July 2001 before been arrested on 2 August 2001 after he voluntarily gave himself up, he was then transferred to the ICTY two days later on 4 August 2001. On 9 August 2001 Kubura was charged by the ICTY on basis of his 'criminal responsibility as hierarchical superior' per Article 7 paragraph 3 of ICTY Statute for six counts of violations of the laws and customs of war per Article 3 of the ICTY Statute including "murder, cruel treatment, wanton destruction of towns and villages not justified by military necessity, plunder of public or private property." Kubura pleaded not guilty to all charges against him the same day. Kubura was given provisional release from 19 December 2001 to 27 November 2003 before his trial officially opened on 2 December 2003. Kubura's defence lawyer Rodney Dixon argued that Kubura was the Chief of Staff and he wasn't officially appointed Commander until 6 August 1993, after the majority of the crimes he was charged with had already been committed. Dixon stated that "there is not much we have to answer in the case against Amir Kubura," and that the prosecution's arguments about Kubura's control of the 7th Brigade over the Foreign Mujahideen were "based on assumptions." On 15 March 2006 Kubura was acquitted for the majority of charges against him however he was found guilty due to his 'superior criminal responsibility' for "failing to take necessary and reasonable measures to punish members of his forces who plundered private or public property in the villages of Susanj, Ovnak, Brajkovici and Grahovcici in June 1993... [and] for failing to prevent or punish members of his forces who plundered private or public property in the village of Vares in November 1993" and he was sentenced to two and a half years imprisonment. The Defence appealed this verdict asking for the verdict to be overturned whilst the Prosecution appealed the sentence requesting that it be increased to five years imprisonment, however the Prosecution's appeal was dismissed by the appeals chamber. Kubura was granted early release on 11 April 2006 due to the 828 days he spent in pre-trial detention. On 22 April 2008 the Appeals Chamber Judges found that Kubura took the necessary and reasonable measures to prevent certain acts of plunder committed by those under his command in Vareš in November 1993 and reversed the Trial Chamber’s charges for this conviction, his sentence was reduced from two and a half years imprisonment to two years imprisonment by the Appeals Chamber; however Kubura had already served his sentence.