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South Sudan became independent from Sudan in 2011 after an overwhelming vote to separate under a 2005 peace plan that followed 22 years of civil war.
An estimated 10,000 people have fled north to Sudan from South Sudan where government troops and rebels have battled for the past month, the UN's refugee agency said on Sunday.
"Ten thousand, this is something we are confident with, that these are confirmed people who have crossed the border, who have been fleeing the conflict," Nicolas Brass, external relations officer with the United Nations High Commissioner for Refugees (UNHCR), told AFP.
The influx marks an ironic turn of events in relations between Sudan and South Sudan, which became independent in 2011 after an overwhelming vote to separate under a 2005 peace plan that followed 22 years of civil war.
Millions of southerners fled north during the civil war, but about 1.8 million had returned to the South since 2007.
As recently as last September, a survey by the International Organisation for Migration found that almost every single one of about 20,000 ethnic southerners still living in squalid Khartoum-area camps wanted to go home.
But that was before fighting began in mid-December with clashes inside South Sudanese army units, sparking a sharp upsurge in ethnic violence.
The new UNHCR figure makes Sudan the second-largest recipient of refugees from the battles between forces loyal to President Salva Kiir and those of his ex vice-president Riek Machar.
About 32,000 refugees have fled to Uganda and a total of around 10,000 others have gone to Ethiopia and Kenya, while more than 350,000 are internally displaced within South Sudan, the United Nations says.
Brass said most of those who have crossed into Sudan are women and children who have reached the Kordofan region where they are "in need of basic assistance".
The UNHCR is working closely with Sudanese authorities who are leading the aid response, he said.
"We've been sending emergency shelter and non-food items" including mosquito nets, sheets and mattresses, Brass said, adding that the 10,000 figure is based on information from local authorities and UNHCR partner agencies.
A UNHCR source said in late December that the agency was investigating reports that hundreds of South Sudanese had fled north.
Last week the UN's Office for the Coordination of Humanitarian Affairs said aid workers were preparing to respond to a possible influx of 10,000 people from South Sudan.
Khartoum's Humanitarian Aid Commissioner was quoted by official media on Friday as saying only 168 "brother Southern Sudanese citizens" had crossed into Sudan.
Brass said the UNHCR is working with the government to prepare for the arrival of thousands more.
"Our planning figure for the time being is 50,000," he said.
The latest refugee arrivals add to an already-strained humanitarian situation in Sudan.
The UN's top official in the country, Ali Al-Za'tari, said last month that a total of 6.1 million people were estimated to need assistance in Sudan, but the UN had received just over half of the funding it had requested.