About 40 bodies were counted at the wreck site by a local reporter.
It is unclear how many of the victims were on the plane and how many were on the ground.
Juba's Radio Miraya says the plane was heading to Paloch in Upper Nile State and crashed just 800m (half a mile) from the runway.
Presidential spokesman Ateny Wek Ateny told Reuters news agency that there were at least two survivors, a crew member and a child.
Cargo planes to remote parts of South Sudan often carry passengers too.
(BBC News)