Beara, 65, told judges at the Hague war crimes tribunal he was not guilty of participation in a conspiracy to commit genocide or the forcible transfer of the population, additional charges in the amended indictment of March 30.
At his initial appearance before the tribunal on November 11, 2004, Beara dismissed charges of genocide and complicity in genocide, extermination, murder and persecution on racial, religious or political grounds.
The initial indictment against Beara was issued on March 26, 2002, and he surrendered to the tribunal on October 10, 2004.
"The accused entered into an agreement between two or more persons to commit the crime of genocide. The accused intended to commit genocide," the amended indictment says.
Beara is one of the chief accused in the massacre of more than 7,000 military-age Bosnian Muslim men, who were taken prisoner by Bosnian Serb forces in the Srebrenica area in July 1995.
Other persons charged with conspiracy are Bosnian Serb overall military commander Ratko Mladic and top officers of the Bosnian Serb army's Drina Corps -- Milenko Zivanovic, Radislav Krstic, Vinko Pandurevic, Vujadin Popovic and Drago Nikolic.
In 2003, the tribunal sentenced General Krstic to 35 years' imprisonment for complicity in genocide. He is serving the sentence in Britain.
All other accused in the case are in the tribunal's custody except Popovic, whose transfer to The Hague has been announced for Thursday, and Ratko Mladic, who is among seven remaining fugitives whose extradition is sought from Belgrade.