Mrksic was sentenced to 20 years' imprisonment for the murder of 194 Croatian prisoners of war at Ovcara after the fall of Vukovar in November 1991.
Captain Miroslav Radic was acquitted of the atrocity, while Major Veselin Sljivancanin's sentence was reduced at appeal from 17 to 10 years. He was released in July 2011, having served two-thirds of the sentence.
Mrksic is the first ICTY indictee who will serve his sentence in Portugal.