His legal counsel in Belgrade said he would not attend on Tuesday unless the lengthy delay was granted, and he would also reject any counsel imposed by the court.
Judges and the prosecution gathered for the start of the trial as scheduled on Monday, but Judge O-Gon Kwon adjourned proceedings less than 30 minutes later as Mr Karadzic's chair remained empty.
"We request Mr Karadzic to attend so that his trial is not further obstructed," he added.
The judge said the court could impose a defence lawyer on Mr Karadzic, among other measures, should he display "consistently obstructive behaviour".
AT THE SCENE
Peter Biles, The Hague
There was a sense of anti-climax as the judges and the prosecution team entered the trial chamber. The chair reserved for Radovan Karadzic was empty. And he had no legal representation in court.
The prosecution made it clear that they're ready for this trial to start. They said there was a choice to either allow Mr Karadzic to represent himself, and frustrate the proceedings, as he has done on Monday, or assign legal counsel to represent him, if he refuses to appear.
After 15 minutes the judge adjourned the proceedings until Tuesday afternoon.
The prosecution called for the tribunal to impose counsel on Mr Karadzic.
Another of his legal advisers, Kevin Jon Heller, said that from the scope of the trial - thought to include 1.2 million pages of evidence, numerous crime scenes and hundreds of witness - it was understandable why Mr Karadzic, who is not a trained lawyer, had stayed away.
"It's deeply regrettable, of course, that he isn't going to be in court, but it's also easy to understand why he isn't.
"He simply doesn't believe there's enough time to prepare his defence."
Mr Karadzic is not due to give his opening statement until next week, after the prosecution has been allowed two days to deliver its opening argument .
Survivors of the conflict were shocked at the delay.
Admira Fazlic had watched the brief proceedings from the public gallery.
"Radovan Karadzic is making the world and justice ridiculous. He is joking with everybody," she was quoted by the Associated Press news agency as saying.
The former president of Republika Srpska, head of the Serbian Democratic Party (SDS) and commander of the Bosnian Serb Army has refused to enter pleas, but says he will co-operate with the court to prove his innocence.
He was indicted in 1995 on two counts of genocide and a multitude of other crimes committed against Bosnian Muslim, Bosnian Croat and other non-Serb civilians during the 1992-1995 war, which left more than 100,000 people dead.
The charges relate to several events, including the campaign of shelling and sniper attacks on Sarajevo during the 44-month siege of the city, in which some 12,000 civilians died.
Mr Karadzic is also accused of being behind the massacre of more than 7,000 Bosniak (Bosnian Muslim) men and youths in Srebrenica in July 1995, and of attacks on more than a dozen Bosnian municipalities in the early stages of the war.
"The prosecution alleges that Karadzic committed all of these crimes together with other members of a joint criminal enterprise with the aim to permanently remove Bosnian Muslim and Bosnian Croat inhabitants from the territories claimed to be a part of the so-called Serbian Republic," the ICTY said in a statement.
Eleven counts of genocide, war crimes, crimes against humanity and other atrocities
Charged over shelling Sarajevo during the city's siege, in which some 12,000 civilians died
Allegedly organised the massacre of up to 8,000 Bosniak men and youths in Srebrenica
Targeted Bosniak and Croat political leaders, intellectuals and professionals
Unlawfully deported and transferred civilians because of national or religious identity
Mr Karadzic faces a maximum sentence of life in prison if convicted.
Correspondents say the judges want to complete the trial by 2012, conscious that the trial of former Yugoslav President Slobodan Milosevic ended without a verdict after four years when he died in custody.
Prosecutors have abbreviated the scale of their case, and will call fewer witnesses and include alleged crimes in fewer locations.
"This trial is important for the victims who will finally see justice being done," chief prosecutor Serge Brammertz told AFP news agency.
"When you speak to a woman who tells you that 21 members of her family have been assassinated, and for some of them she even has no idea where the bodies are, you can easily measure the importance of this trial."
Mr Brammertz said his only regret was that the former Bosnian Serb military leader, Ratko Mladic, would not be in the dock on Monday.
When Mr Karadzic was found living disguised and under a false name in Belgrade in July 2008, some officials claimed that Gen Mladic would be next. But more than a year on, Gen Mladic is still at large.
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