"This is not an issue that can simply be dismissed as a bilateral agreement between me and the United States. He (Holbrooke) acted on behalf of the permanent members of the security council."
Bonomy warned Karadzic of the dangers inherent to conducting his own defence, particularly with regard to Karadzic's submissions on the issue of indemnity.
The trial court was considering his claims, said Bonomy, to determine whether any agreement with Holbrooke "can have or ought to have an influence on the work of an independent tribunal".
"I hope you took legal advice when you made your representations and that you didn't sell yourself short in this particular matter," the judge told Karadzic.
The 63-year-old faces 11 charges of genocide, war crimes and crimes against humanity, notably for the 44-month siege of Sarajevo that left 10,000 dead and the July 1995 massacre of 8,000 Muslim men and boys in Srebrenica.
Alan Tieger, the prosecutor, told the court that a new indictment would be filed by Monday. No details were disclosed as to whether this would include new or amended charges.
Holbrooke, the architect of the Dayton peace agreement that ended Bosnia's 1992-95 war, has denied cutting a deal with Karadzic.
Karadzic was arrested on a Belgrade bus in July this year after 13 years on the run.
At the time, he was disguised with white hair and a beard and working as a new age healer under the assumed name of Dr Dragan Dabic.