Services for refugees could be hit when UN peacekeepers leave Chad later this year, the UNHCR says.
A spokesman for the UN refugee agency told the BBC that he "regretted" the decision to withdraw the peacekeepers from Chad and Central African Republic.
The 4,375-strong force is to pull out in stages by the end of 2010.
It was deployed in 2009 to protect hundreds of thousands of displaced Chadians and refugees from the Sudanese province of Darfur.
The Chad government has asked the UN Security Council to withdraw the peacekeepers.
"We understand the reasons behind [the decision] but we are concerned for the consequences for our operations in eastern Chad," UNHCR spokesman Mans Nyberg told the BBC's Network Africa programme.
"When they leave, we might have to restrict our operations."
Mr Nyberg said there were daily attacks in eastern Chad, which remains "very volatile".
He said the UN troops were more able to provide security than Chadian forces.
Chad is home to 260,000 refugees from Sudan's war-torn Darfur region, which is just across the border.
Amnesty International has also warned that the UN decision could endanger the refugees.
Its Africa programme director Erwin Van Der Borght told the BBC that the situation had not "changed fundamentally" since the decision was taken for the UN to take over from an EU peacekeeping force.
About one-third of the UN force, known as Minurcat, will begin leaving in July, and the final pull-out is to commence in October.
The mission currently has 3,300 military and 1,075 civilian personnel in Chad and the Central African Republic.
France also has two military bases in Chad with about 1,000 troops. These are not involved in peacekeeping operations but have occasionally intervened to protect the government against rebels.
Chadian President Idriss Deby said earlier this year that the UN force was no longer necessary, describing it as a failure.
The decision to withdraw does come at a time of thawing relations between Chad and Sudan - previously a major source of conflict in the region.
However, last month there were clashes in eastern Chad, with the government saying it had killed more than 100 rebel fighters.