Based on the plea agreement, Rajic will be rearraigned at 3 pm on Wednesday.
The 47-year-old Rajic is charged with 10 counts of violations of the laws and customs of war and grave breaches of the Geneva conventions for the murder of some 30 Muslims in Stupni Do on 23 October 1993 and for the unlawful detention and torture of civilians in Vares that September.
Rajic was first indicted in 1995 and was arrested in Split, Croatia, on 5 April 2003. He was transferred to The Hague on June 24. During his first arraignment on June 27, he pleaded not guilty and did the same on 29 January 2005 after the indictment was amended.
Rajic's decision to reach a plea agreement with the Office of the Prosecutor caused a rift with his attorney Zeljko Olujic. He is now represented by Doris Kosta.
Both attorneys had told Hina before that a plea agreement was being prepared.
Earlier this year, the Office of the Prosecutor proposed referring the Rajic case to the judiciary of Bosnia and Herzegovina.
After Miroslav Bralo, who did so in July, Rajic is the second Bosnian Croat accused by the Hague tribunal to reach a plea agreement with the prosecutors.
The details of the plea agreement will be revealed tomorrow.