On Wednesday, a convoy of the World Food Programme was attacked by unidentified gunmen in Shambe of Lakes state. One person was killed and four others were wounded.
One cargo vessel sank due to the gunfire.
In a statement, UN Humanitarian Coordinator Alain Noudéhou said he strongly condemned the attack and called for an end to repeated acts of violence which are disrupting life-saving assistance to flood-affected people.
Mr. Noudéhou called on the Government and all parties to protect humanitarians and those supporting efforts to help millions of people in need.
Some 800,000 people have been affected by flooding in South Sudan since July. Almost half of all the counties in the country are affected, with many areas underwater.