The Sudan Tribune reported Sudanese warplanes bombarded Bentiu, the capital of Unity state, and Rubkotna, killing at least three people.
The reported attacks came three days after South Sudan said it was withdrawing troops from a strategic oil field in a disputed border region, China's state-run news agency Xinhua reported.
"These accusations are baseless," Sudanese Armed Forces spokesman al-Sawarmy Khalid Saad told Xinhua. "We do not accept any accusations on aerial bombardments [or] ground attacks in Unity state."
News of the bombing came after some of the worst fighting between the two countries over the oil-rich Heglig. South Sudan claimed the town about two weeks ago, then lost it to Sudan on Friday.
"Since we have liberated Heglig area, we have not advanced a single step into South Sudanese territories. We have never bombarded any areas in South Sudan and we have nothing to do with what is going on in Unity state," Saad said.