The Satellite Sentinel project says the apparent massacre took place in the town of Kadugli, in South Kordofan.
Fighting began in the state last month, between rebels from the Nuba mountains and the Sudanese armed forces.
A Sudanese military spokesman denied allegations that civilians had been killed.
South Kordofan borders South Sudan, which last week became an independent state.
Some 70,000 people have fled the recent fighting there.
The Satellite Sentinel project says the satellite images are consistent with allegations the Sudanese armed forces and government-aligned militias have targeted civilians.
A recent UN report said bombing and fighting was continuing in South Kordofan despite a peace deal.
The BBC's James Copnall in Sudan's capital, Khartoum, reports that it is extremely difficult to get accurate information, as journalists and diplomats are barred from the region and the UN faces restrictions on its movement.
The images released by the Satellite Sentinel Project show three apparent mass graves, it says. (read more)