The deaths were reported by independence leader, Jose Ramos Horta, and were carried by international news agencies, the spokesman added.
But UN officials and representative of CARE International and Asistencia Medica Internacional (AMI) visited the area on Thursday and concluded there had been no deaths from hunger. AMI runs a mobile clinic in Manatuto.
Aid agencies delivered 375.5 metric tonnes of food to the six districts of the region over the past two months, the spokesman added.
"The UN is concerned that the inaccurate report could further impede the return from West Timor of refugees who have already been the target of a misinformation campaign intended to discourage them from returning," the spokesman said.
Meanwhile, the UN Interim Administrator in East Timor, Sergio Vieira de Mello, is due in Thailand on Friday to hold talks with the government and business leaders.