"Based on an analysis of DigitalGlobe satellite imagery and eyewitness reports obtained by the Satellite Sentinel Project, SSP has identified a site consistent with mass graves in Kadugli," said the monitoring group set up by Hollywood star and rights activist George Clooney on Thursday.
Eyewitnesses say the Sudanese Armed Forces and government-aligned militias conducted house-to-house searches, systematically killing suspected supporters of the ex-rebel Sudan People’s Liberation Army of the south.
The conflict between the two sides, which first erupted on June 5, has showed no signs of abating, and Kadugli itself has been the scene of some of the fiercest fighting.
Activists say the army is implementing a government policy of ethnic cleansing, targeting the state's indigenous Nuba peoples, many of whom fought with the SPLA during their decades-long war with Khartoum.
Citing eyewitnesses, SSP said dead bodies had been picked up from the market area of Kadugli, and from the nearby villages El Gardud and Tilo, and dumped in open pits less than a kilometre (mile) south of the Tilo Secondary School.
"(An) eyewitness said... he estimated that 100 or more bodies were deposited at the site on the evening of June 8," the monitoring group said.
"As of July 4, three excavated areas measuring approximately 26 by five metres are visible less than one kilometre south of the Tilo school," it added.
Sudan's President Omar al-Bashir on Tuesday vowed to bring political stability and development to the state's of Blue Nile and South Kordofan, which both have large numbers of SPLA supporters.
On the same day, the UN humanitarian office reported heavy bombardments and gunfire in different areas of South Kordofan over the past week, including around Kadugli, dimming the prospects of any imminent political settlement.