Karadzic complained of not having a defence team and that he was being left on an uneven footing with the court.
The judge said that if Karadzic is having trouble keeping pace with proceedings, it is his own fault for choosing to defend himself.
Bonomy said that prosecutors are still waiting for the court to approve planned changes aimed at streamlining Karadzic's indictment, a process likely to take several weeks.
While Karadzic is entitled under the United Nations court's rules to defend himself, the tribunal fears his decision could lead to a repeat of the defects in the trial of Slobodan Milosevic, his one-time political mentor and the former Yugoslav president.
Acting as his own counsel, Milosevic prolonged his genocide trial for four years before the case was aborted without a verdict when he died of a heart attack in his UN jail cell in March 2006.
With that in mind and pointing out the complexity of the case, Bonomy has repeatedly urged Karadzic to hire an attorney.
He tentatively set January 20 as a date for a new status conference.
Prosecutors said Karadzic will be supplied with the amended indictment's supporting material by the end of the week, after which he will have 14 days to respond.
If the court decides to accept the amended charges, Karadzic will need to enter a new plea.