The decision was made after Jelavic, as the first defendant in the so-called "Croat self-rule" case, failed to appear before judges on Thursday.
The three men are charged with undermining the military and defence power of the country and abuse of office and authority.
Prosecutor Drew Engel proposed separation of the proceedings, arguing that a trial might never start if the court were to wait for all three men to appear in the courtroom at the same time. He also noted that the Criminal Code of Bosnia-Herzegovina did not provide for trials in absence.
In light of the new situation, the trial chamber accepted a defence motion and gave the prosecutor 15 days to draft a new indictment against Prce and Curcic.
Judge Pietro Spera scheduled the next hearing for 7 November, announcing that he would order judicial police to arrest Jelavic and bring him to the court.