Twenty-nine of the children drowned after running into swamps to hide from attacks in Leer County. There were reports of widespread use of sexual violence, including more than 50 rape cases, said the Protection Cluster, representing 60 local and international organisations.
South Sudan's military spokesman, Col Philip Aguer, said today that he had no reports of fighting in Leer County.
The UN and human rights groups have documented widespread abuses against civilians, including rapes and killings by government soldiers and their militia, in Unity state this year. Fighting persists despite a peace deal signed in August.
"As a result of this new wave of violence, it is estimated that nearly 1,200 children are unaccompanied and separated in southern and central Unity State," the Protection Cluster said.
South Sudan has been at war since December 2013 as government forces loyal to President Salva Kiir, an ethnic Dinka, battle rebels led by his former deputy, Riek Machar, a Nuer. The fighting has often been along ethnic lines.