Over 2,000 people have been killed in cattle raids this year as security worsens, threatening the fragile north-south peace deal.
MSF said that a greater response was needed to meet the needs of hundreds of thousands of people displaced by the fighting.
"Violence is surging, plunging people from one disaster to the next. Yet immediate needs are not being met," said Stephan Goetghebuer, MSF director of operations for Sudan.
"A better response to this growing emergency is crucial, or clinics will continue to run out of vital medicines, gunshot patients will still reach medical care many days after attacks and countless others will receive no care at all."
Ugandan rebel group the Lord's Resistance Army (LRA) has also attacked civilian settlements this year.
MSF called on governments, donors and aid agencies to recognize the full scale of the crisis.
A shift in the nature of the violence this year - which usually claims the lives of men guarding their cattle - has seen more women and children killed.
Many in Southern Sudan believe that Khartoum is orchestrating the violence in order to undermine Southern Sudan's progression toward full independence.
Others say the clashes are being stoked by southern political rivals.
A fragile peace has held between north and south since the end of a 21-year civil war in 2005.
The peace deal that ended the war laid out a road map that included elections in Southern Sudan, to be held next year, and a referendum on independence in 2011.
However, the UN is warning that if the violence continues, it will be difficult to organize the crucial ballot in the south. dpa ml ncs