Judge O-Gon said he had warned Karadzic he must accept the consequences of refusing to be at his trial and that the court will decide how to proceed next week.
Karadzic, who opted to defend himself in the trial despite having no legal background, now says he needs more time to prepare his defence.
The ICTY heard the first part of the prosecutor's opening statements on Tuesday, during which Karadzic was described as the "supreme commander" of an ethnic cleansing campaign in the 1992-5 Bosnian war.
Alan Tieger, a senior prosecutor at the court, quoted Karadzic as saying before the war that Serb forces would turn Sarajevo into "a black cauldron, where 300,000 Muslims will die".
He said witnesses who survived the deadly 44-month siege of the city would describe living "in constant fear, day after day, for years, knowing that they or their loved ones were targets".
Tieger added that the case was about a "supreme commander, a man who harnessed the forces of nationalism, hatred and fear to implement his vision of an ethnically separated Bosnia".
Parampreet Singh from Human Rights Watch told Al Jazeera the prosecution's use of Karadzic's own words was an interesting way of attempting to prove their case against him.
"Through the telephone intercepts, through the various internal documents and speeches given in rallies - they're using that information to show ... the extent to which [the prosecution allege] he was in control of devising the policies that led to the widespread commission of crimes against non-Serbs in Bosnia," she said.
Karadzic faces 11 counts of genocide, war crimes and crimes against humanity for allegedly masterminding Serb atrocities during the 1992-95 Bosnian war, a conflict that claimed an estimated 100,000 lives.
Among the charges Karadzic faces is one count of genocide over the massacre of Muslim men and boys at the UN-protected enclave of Srebrenica in July 1995, in which about 8,000 people died.
He also faces another genocide charge over the siege of Sarajevo, the Bosnian capital.
Tim Friend, Al Jazeera's correspondent at The Hague, said the prosecution "feel they have substantial evidence linking Radovan Karadzic to these horrendous events during that bloody war".
"He [the prosecutor] said Karadzic was a man who spread hatred, had no regard for humanity and that his hand was at the helm, that he was in charge when events like Srebrenica took place.
"He [the prosecutor] said he [Karadzic] was in charge, and directly ordered, the siege of Sarajevo, when civilians were deliberately targeted ... and was also responsible, directly, on his orders, for the taking of UN peacekeepers as human hostages against further attack against the Bosnian Serbs."
Caught in disguise
|Karadzic had been posing as a healer when he was caught in Belgrade [EPA]
Karadzic has repeatedly refused to enter pleas, but insists he is innocent.
According to the charge sheet, he stands accused of having "participated in an overarching joint criminal enterprise to permanently remove Bosnian Muslim and Bosnian Croat inhabitants from the territories of Bosnia-Hercegovina claimed as Bosnian Serb territory".
His trial is expected to last for up to two years and he faces a maximum sentence of life in jail if convicted.
Karadzic was arrested in Belgrade last July after 13 years on the run.
He had been posing as a New Age healer named Dr Dragan Dabic, and had disguised himself with thick glasses, a bushy beard and straggly grey hair.
Prosecutors had wanted to try Karadzic alongside his wartime military chief, General Ratko Mladic, but he has yet to be caught.
He is one of two suspects still sought by the court, the other being Goran Hadzic, a former leader of Serb fighters in Croatia.