Cermak left the ICTY compound shortly before 4 PM on Friday through a special exit and reporters did not see him leaving the detention centre.
After acquitting Cermak of all counts, the ICTY trial chamber ordered his immediate release.
The two other indictees in the case -- General Ante Gotovina and General Mladen Markac -- were found guilty of eight counts in a nine-count indictment. Gotovina was sentenced to 24 years in prison and Markac got 18 years for war crimes during Operation Storm, when Croatian forces reclaimed areas held by Serb rebels in August 1995.
The verdicts are subject to appeal.