UN agencies say some 160,000 people have been displaced in the past few months in the districts of Mullaittivu and Kilinochchi as the government steps up its offensive against Tamil Tiger rebels.
Some 70,000 people have fled due to fighting in the past two months alone.
UN agencies began pulling out of the region on Thursday after Colombo said it could not guarantee the safety of aid workers.
"We have temporarily suspended withdrawing our staff, vehicles and other equipment.
Large groups of civilians continue to block our offices in the Wanni since Friday," UN spokesman, Gordon Weiss told AFP.
He said thousands of men, women and children were protesting outside UN and other international aid agency offices in Kilinochchi to stop aid workers from leaving.
"The Sri Lankan government is very much aware of the present situation," he said, adding that the UN's Colombo offices were waiting further instructions from their headquarters in New York.
The Liberation Tigers of Tamil Eel