The Antonov aircraft went down on Tuesday night near Wadi Seidna air base, one of the army's largest military hubs in Omdurman, northwest of the capital.
The army, which has been at war with the paramilitary Rapid Support Forces (RSF) since April 2023, said the plane crashed during takeoff, killing and injuring both military personnel and civilians.
"After a final tally, the number of martyrs reached 46, with 10 injured," the Khartoum regional government's media office said in a statement.
The army-aligned health ministry had previously reported at least 19 dead.
Witnesses described hearing a loud explosion and seeing several homes damaged in the area. The crash also caused power outages in nearby neighbourhoods.
The ministry said emergency teams rushed injured civilians, including children, to a nearby hospital.
A military source cited a technical malfunction as the cause of the crash, speaking to AFP on condition of anonymity because they were not authorised to comment to the media.
- Army advances -
The crash came a day after the RSF claimed responsibility for shooting down a Russian-made Ilyushin aircraft over Nyala, the capital of South Darfur
The paramilitary group said the plane was destroyed with its crew onboard.
The recent escalation follows significant advances by the army in central Sudan and the capital Khartoum in its multi-front offensive against the RSF.
Late on Saturday, RSF signed a charter with allied political and armed groups in Nairobi, Kenya, paving the way for the formation of a parallel government in rebel-held areas.
Since April 2023, army chief Abdel Fattah al-Burhan and his former deputy and RSF commander Mohamed Hamadan Daglo, once allies, have been locked in a deadly power struggle.
The war, which has claimed tens of thousands of lives, erupted after a rift emerged between Burhan and Daglo over the future structure of the government.
The conflict has triggered one of the world's worst humanitarian disasters in recent memory, according to the United Nations.
The fighting has devastated Khartoum and other major cities, displacing over 12 million, plunging the country into hunger and crippling critical infrastructure.
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