The alleged highly enriched uranium (HEU) project has become a key issue as the United States and other countries press the communist nation to honour its pledge to scrap all nuclear programmes.
"I have no doubt that North Korea has had a highly enriched uranium programme, and that has been and continues to be the judgement of our intelligence community," he told a news conference here.
"We would expect that when North Korea makes its declaration of nuclear facilities, that that would be one of the issues addressed in North Korea's declaration."
Seoul is the final stop on the deputy secretary's Asian tour, which is focussed on getting North Korea to abide by its commitment made at six-nation talks on February 13.
US intelligence officials last week publicly softened their position on the HEU programme, admitting to doubts about how much progress had actually been made.
A 1994 deal which shut down the North's plutonium-producing reactor collapsed after the Bush administration confronted the North about the alleged HEU project in 2002.
Over the past five years the North is thought to have produced enough plutonium to make several more bombs. It tested its first nuclear weapon last October.
Under the February six-nation agreement, the North must declare and disable all its programmes in exchange for diplomatic benefits and economic aid equivalent to one million tons of fuel oil.
The visit by the number two US diplomat to Japan, China and South Korea is his first official overseas trip since taking office last month. It is part of a round of intense diplomacy aimed at following up on the accord.
Washington's chief envoy to the nuclear talks Christopher Hill began holding two days of meetings in New York on Monday with his North Korean counterpart Kim Kye-Gwan on ways to normalise diplomatic relations as part of the pact.
On Wednesday Japanese and North Korean negotiators are due to start talks in Hanoi on normalising ties.
The six-nation talks group the two Koreas, Japan, Russia, the United States and host China.