The prosecution did not provide any evidence that would corroborate the allegations in the indictment, the president of the panel of judges, Jasenko Ruzic, said handing down the verdict.
The indictment, which the cantonal prosecutor's office filed in June 2011, accused Covic of helping the Lijanovici company from Siroki Brijeg illegally make a little under one million euros in 2000-01.
The verdict can be appealed with the Federation Supreme Court.
Covic was already tried for this case at the Bosnian State Court, which found him guilty in 2006 of abuse of office and sentenced him to five years' imprisonment. The appellate court quashed the sentence in 2008, ruling that the State Court was not authorised to deal with the case which was transferred to the judiciary of Sarajevo Canton.