A statement from the UN said that it suspected the Liberation Tigers of Tamil Eelam (LTTE) were involved in the theft from buildings it had left on the orders of the Sri Lankan government.
The UN did not disclose what was stolen, but local media reported that the suspected rebels took large stocks of fuel and electricity generators.
UN and other international agencies pulled staff out of the tense area near the rebel political capital Kilinochchi after the government said it could not guarantee their safety.
Fighting has escalated around the rebel-held Wanni region, comprising Kilinochchi and Mullaittivu, as security forces fight to dismantle the Tigers' northern territory.
"The UN has drawn this to the attention of the LTTE and says that humanitarian assets and staff ought to be protected at all times in accordance with international