David Gressly, regional coordinator for the U.N. mission, said at least four militant groups are threatening peace in the region. The Sudan People's Liberation Army, the south's army, has launched military offenses aimed at containing each group.
"While the government of southern Sudan has a responsibility to address a security threat within its territory, we urge it to do so in accordance with international humanitarian law," he said in a statement.
Gressly said the primary issue is related to incomplete processes of reintegration of forces following the end of civil war in Sudan.
South Sudan in January voted to become an independent nation. Issues like border demarcation and the sharing of natural resources remain unsettled.
A comprehensive peace deal reached in 2005 ended a civil war that killed an estimated 2 million people.
Francis Deng and Edward Luck, U.N. special envoys on the prevention of genocide, said in a statement in early conflict in the disputed region of Abyei remains a flash point for renewed Sudanese conflict.
Clashes between rival groups in Abyei have left more than 100 people dead and displaced at least 20,000 people, the United Nations said.