On 18 July 2007, the Court of Bosnia and Herzegovina rendered a first instance verdict acquitting the accused of war crimes against civilians and crimes against humanity alleged to have been committed in April 1992. Mandić had been charged with having, in his capacity as Republika Srpska's deputy minister of the interior, planned and ordered an attack against a training centre of the Ministry of the Interior of the Republic of Bosnia and Herzegovina, and of having incited and aided in the subsequent inhumane treatment of the centre's staff. The court found that it had not been established that on the date of the attack, the accused had held, whether de jure or de facto, the office of deputy minister of the interior, or that he had acted as a superior over the members of the police who had detained, interrogated and physically abused the victims. The court also concluded that at the time of the attack, on 4 April 1992, there was not yet an armed conflict within the meaning of Article 3 common to the 1949 Geneva Conventions, the Panel having accepted as proven the fact that the armed conflict broke out after Republika Srpska was recognized on 6 April 1992.
Mandić was also acquitted of crimes against humanity. In his capacity as minister of justice of Republika Srpska, he was charged with personal and command responsibility for crimes committed in the correctional institutions under the control of Republika Srpska. The Trial Panel concluded that it had not been proved beyond a reasonable doubt that he had personally committed the criminal offences he was directly charged with, nor that he had exercised effective control over the subordinates who committed the offences or were about to commit them.
The verdict was upheld by the Appeals Chamber on 1 September 2009. The Court having reviewed the Appeal by the Prosecutor's Office of BiH and the responses to the Appeal at a session of the Panel of the Appellate Division held on 1 September 2009, rendered the Second Instance Verdict refusing the Appeal by the Prosecutor's Office as unfounded and upholding the First Instance Verdict dated 18 July 2007.