He said the UN Mission (Unmiss) protected hundreds of civilians around the country.
"I have no doubt that thousands of civilians would not be alive today if not for the presence of of Unmiss."
The security, economic and humanitarian situation had worsened dramatically since last year and the conflict had intensified, Shearer has told the council.
He said more than 15,000 civilians fleeing violence and sought shelter from Unmiss in recent months.
Multiple witnesses reported the Sudan People's Liberation Army had shot many people after asking their ethnic groups, he said.
Government forces had also torched houses, hospitals and schools, and targeted men and boys along ethnic lines. Sexual violence was also rife, Shearer told the council.
He said a third of South Sunan's population was displaced or are refugees.
"This is a manmade disaster. Three years of conflict has eroded their livelihoods, prevented them from harvesting and caused cattle to be looted on a grand scale."
However, Shearer also paid tribute to aid workers. Recent attacks have killed 10 aid workers as humanitarian bases are looted and attacked.