Former Bosnian Army commander Sefer Halilovic has been cleared of claims he was responsible for the killings of Croat civilians in 1993.
Sefer Halilovic denied the charges against him
The UN war crimes tribunal at The Hague said prosecutors had failed to prove that he was in charge of troops who carried out the killings.
Mr Halilovic was the highest-ranking Muslim army officer to be tried for war crimes relating to the conflict.
He was a minister in the Bosnian government when he surrendered in 2001.
The charges related to killing of at least 62 civilians in the villages of Grabovica and Uzdol. They were occupied during an operation by Muslim forces to retake areas held by Bosnian Croats in a bid to end the blockade of Mostar.
The indictment alleged that Mr Halilovic had ordered the deployment of two army units from Sarajevo with "notorious reputations for being criminal and uncontrolled in behaviour".
Judges at the International Criminal Tribunal for the former Yugoslavia (ICTY) ordered the release of Mr Halilovic, who had denied the charges.
In March, the man who succeeded Mr Halilovic as Bosnian Army Commander in 1993 pleaded not guilty to war crimes charges at the tribunal.
Rasim Delic, 56, has been indicted over crimes said to have been carried out by foreign fighters, or mujahideen, he commanded during the 1992-1995 war in Bosnia.
The alleged crimes include the murder and torture of Bosnian Serbs and Croats and the rape of female prisoners.