"Warplanes launched intensive strikes targeting residential areas, including the Al-Sad Al-Ali, Al-Riyadh, and Texas neighborhoods" earlier in the day, an eyewitness told Xinhua by phone.
"An air strike also targeted the popular Al-Malaja market in Nyala," the eyewitness said.
The eyewitness said about 40 civilians were killed in the airstrikes.
The Al-Wohda health center in Nyala received "a large number" of trauma patients, some of whom were already dead when rushed there while some others died after arrival, a medical cadre at the center told Xinhua.
He said the number of fatalities could further increase.
Also on Wednesday, the paramilitary Rapid Support Forces (RSF) issued a statement accusing the Sudanese Armed Forces (SAF) of targetting civilians in air raids in the state capital, killing 40 people and injuring hundreds.
The RSF further said that the search is still continuing for bodies under the rubble.
A comment could not be obtained yet from the office of the SAF spokesman.
Sudan has been witnessing deadly clashes between the SAF and the paramilitary Rapid Support Forces (RSF) in Khartoum and other areas since April 15, resulting in at least 3,000 deaths and more than 6,000 injuries, according to the Sudanese Health Ministry.