Some 70,000 people have fled due to fighting in the past two months alone.
The withdrawal came as the island's government said it was on track to capture the rebels' political capital Kilinochchi by the end of the year.
"All expatriate and local staff who are not from Kilinochchi and Vavuniya have been moved out today (Tuesday)," UN spokesman in Colombo, Gordon Weiss, told reporters.
He did not say how many staff were withdrawn in total.
Fighting has escalated along the tense northern frontier as security forces forge ahead to capture Kilinochchi.
"We are unable to guarantee their (aid workers') safety any more.
That is why they have to leave," Sri Lankan President Mahinda Rajapakse told foreign correspondents based in Colombo late on Monday.
"They (UN and other aid agencies) can return after the army says it is safe," said Rajapakse, who is also the island's defence minister.
However, the Liberation Tigers of Tamil Eelam (LTTE) warned of a "humanitarian crisis" if the UN wo