A soldier was killed and three others wounded in internal fighting between forces linked to Abdel Fattah al-Burhan in Omdurman on Saturday, police sources said.
The clash broke out at Sabreen market during routine duties, escalating rapidly from a dispute into an exchange of gunfire.
Two personnel were initially injured, one suffering a hand wound and another hit by shrapnel in the neck.
A critically wounded soldier later died in hospital after sustaining a severe neck injury in the confrontation.
Authorities have opened an investigation to establish the cause of the clash and determine responsibility.
