The Bangladeshi scuba divers, from the United Nations peacekeeping force, were scouring the White Nile river around the crash site, the UN mission said.
South Sudan's transport minister said they were trying to establish what caused yesterday's crash, when the Soviet-era Antonov plane smashed into a river bank just after take-off from the capital Juba.
"Our main target now is to uncover all the dead bodies and the black box, and we can launch a full investigation into the crash," Kwong Danhir Gatluat said.
The main fuselage of the plane ploughed into thick woodland but the debris was scattered over a wide area around the riverbank, as well as into the river itself.
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Police said they did not know how many had been on board the plane when it crashed - nor if anyone had been killed or injured on the ground - and so were unable to give an official death toll.
Juba's airport is the busiest in the war-torn country, which is the size of Spain and Portugal combined but has only a few paved roads.
The airport hosts regular commercial flights, as well as a constant string of military aircraft and cargo planes delivering aid to remote regions cut off by road.