"We have not got any reason as to why. We are in discussion with the government," said Sarah Crowe, UNICEF's head of communications for South Asia.
However, in an interview with Al Jazeera, Palitha Kohona, Sri Lanka's foreign minister said news that Elder was being expelled was incorrect, although his visa status had been placed under review.
"There's a rule that UN officials follow and it's a rule that is followed invariably - they do not get involved in domestic politics," he said.
"Unicef is talking to us and we will continue to talk to Unicef."
Sri Lankan soldiers defeated the Tigers in May, ending one of Asia's longest civil wars.
|Sri Lankan forces defeated the Tamil Tiger rebels in May [Reuters]
Before the government's defeat of the Tigers, Elder spoke of the "unimaginable hell" suffered by children caught up in the last stages of the war.
According to UN estimates the decades-long war left between 80,000 and 100,000 people dead.
As fighting peaked earlier this year during the Sri Lankan army's final offensive, the UN and human rights groups said an increasing number of civilians, many of them children, were caught in the crossfire.
During the war the Sri Lanka government maintained tight control of media coverage of the fighting, banning virtually all access to the conflict zone in the northeast and issuing few visas to international reporters.
More than 280,000 Tamil civilians are now being held in military-run displacement camps with the government maintaining tight restrictions on access by aid groups.