After Jovic entered his plea, Judge Aphonse Orie said he would not be taken into detention and told the Slobodna Dalmacija daily journalist that he was free to return to Croatia.
The judge said a warrant for Jovic's arrest had been issued only to ensure his appearance before the tribunal.
Jovic pleaded not guilty to the indictment charging him with publishing the identity and testimony of a protected witness from the Tihomir Blaskic trial.
Jovic, former editor-in-chief of Slobodna Dalmacija daily, was arrested on 6 October by Croatian police, acting on the 28 September arrest warrant issued by the Tribunal, after he failed to appear in court.
Jovic's defence attorney said that in about ten days he would file a preliminary motion to contest the tribunal's jurisdiction in cases of contempt of court.
Judge Orie said a trial date would depend on a motion for a jointer of Jovic's case with that of another three Croatian journalists indicted for contempt of court, which consisted of publishing a classified testimony and revealing the name of a protected witness during the Tihomir Blaskic trial
Prosecutor David Akerson said he would forward all documents regarding the indictment to Jovic and his attorney, while Judge Orie ordered Jovic not to publish the materials.
Orie also warned Jovic that he was obliged to to comply with ICTY summonses in the future or that another warrant for his arrest would be issued.