Officials warned of a "full-blown catastrophe" if fighting does not end.
A further 334,000 people have been displaced within Sudan.
Fighting is continuing in the capital, Khartoum, between the army and the paramilitary Rapid Support Forces (RSF), despite a ceasefire due to be in force.
Diplomatic efforts are being stepped up to try and get the warring parties to the negotiating table.
On Tuesday, South Sudan's foreign ministry said the army and RSF had agreed "in principle" to a new seven-day truce from 4 May, and had promised to send representatives to talks.
Its statement came a day after the UN special envoy to Sudan, Volker Perthes, told the AP news agency that the two sides had agreed to negotiate a "stable and reliable" ceasefire.
Saudi Arabia was a potential venue for the talks, he added.
If talks take place, it would be the first meeting between the two sides since the conflict started.
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More than 500 people have been killed and more than 4,000 have been wounded in the fighting, according to Sudan's health ministry.
A series of temporary ceasefires have failed to hold, with the military continuing to pound Khartoum with air strikes in a bid to weaken the RSF.
The paramilitary group said it shot down a MiG fighter jet over the city, but there is no independent confirmation of the claim.
Heaving fighting has also taken place in Darfur in western Sudan.
UN refugee agency spokeswoman Olga Sarrado told reporters in Geneva that the 100,000 total included people from Sudan, South Sudanese citizens returning home, and people who were already refugees within Sudan fleeing the fighting.
Refugees have also been fleeing over Sudan's border with Egypt in the north and Chad in the west.
Most European states have completed the evacuation of their nationals, but Russia said on Tuesday that it was sending four military planes to fly out more than 200 people - including its nationals and those from "friendly countries" - from Sudan.
In Khartoum, food, water and electricity are running out, but desperately needed aid supplies - shipped by the UN into Port Sudan - are being warehoused because of the violence. Meanwhile, widespread looting means there is no safe way to deliver them.
World Health Organization (WHO) regional director Ahmed al-Mandhari said that health facilities have come under attack in Khartoum, and some are being used as military bases.
"Up to now there were around 26 reported attacks on healthcare facilities. Some of these attacks resulted in the death of healthcare workers and civilians in these hospitals," he told the BBC.
"Also you know some of these hospitals are used as military bases and they have thrown the staff, they have thrown patients out of these healthcare facilities," he added.
On Monday, the UN's Humanitarian Coordinator in Sudan, Abdou Dieng, said that more than two weeks of devastating fighting risked turning the country's humanitarian crisis into a "full blown catastrophe".
"Even before the current crisis, one-third of Sudan's population, nearly 16 million people, already needed humanitarian aid. Some 3.7 million people were already internally displaced, mostly in Darfur," he said.
By Farouk Chothia in London & Imogen Foulkes in Geneva