The bombing in the south of Sudan's capital came about a week after another air strike, also in southern Khartoum, killed 20 civilians on September 2, according to activists.
The number of victims in Sunday's "Qouro market massacre" had risen to 46 by evening, said the local resistance committee, one of many groups that used to organise pro-democracy protests and now provide assistance during the war.
In its statement, the committee revised an earlier toll of 30 killed. It added there were "dozens wounded" and said casualties continued to pour into the nearby Bashair hospital.
"At about 7:15 am (0515 GMT), military aircraft bombarded the Qouro market area," the committee said.
The hospital had issued an "urgent appeal" for all medical professionals in the area to come and help treat the "increasing number of injured people arriving".
A conservative estimate from the Armed Conflict Location & Event Data Project says nearly 7,500 people have been killed in the war that began on April 15 between army chief Abdel Fattah al-Burhan and his former deputy, Mohamed Hamdan Daglo, who commands the paramilitary Rapid Support Forces (RSF).
In early July an air strike on a residential area of Omdurman, Khartoum's sister city, killed around two dozen people and drew condemnation from the United Nations.
- Millions uprooted -
The armed forces control the skies over Khartoum, while RSF fighters continue to dominate the city's streets.
The army has been accused of repeated indiscriminate shelling of the residential areas where the paramilitaries have embedded themselves, including by evicting families and taking over homes.
Positioning themselves in civilian occupied neighbourhoods and buildings is "a potential violation of the Geneva Conventions," the US-supported Sudan Conflict Observatory has said.
It added that the Sudanese Armed Forces "would still be required to ensure that civilian harm is minimised regardless of whether a target has been made a legitimate military target."
On Sunday RSF accused the military of the "air strikes against civilians in the south of Khartoum."
The armed forces denied attacking the market, saying it "directs its strikes against rebel gatherings, crowds and bases as legitimate military targets, and fully adheres to international humanitarian law."
In addition to the capital, fighting has been mainly been concentrated in the western region of Darfur.
Western countries have accused the RSF and allied militias of killings based on ethnicity in Darfur, and the International Criminal Court has opened a new probe into alleged war crimes.
After months of combat, neither side has been able to seize a decisive advantage.
UN data show that around 2.8 million people have fled the Sudanese capital, whose pre-war population was around five million.
Those who cannot or refuse to leave Khartoum remain trapped by air strikes, artillery fire and street battles, forced to ration precious water and electricity.
A total of more than five million people have been forced to flee their homes in Sudan, according to the UN, one million of them across borders.
In the early months of the war, truces brokered by the United States and Saudi Arabia were systematically violated before the two mediators adjourned talks in June.
Recent moves by Burhan, including trips to Egypt, South Sudan and Qatar, signalled a potential return to diplomacy, though both he and Daglo continue to trade hostile statements.
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