"This is the first step for the North's nuclear abandonment," Song Min-Soon said in Seoul.
"Once the disablement is completed, it would take North Korea a considerable period of time to restart the facilities."
The visit is the second by US nuclear experts this month and comes as Washington pushes North Korea for concrete progress on disarmament steps in the next 60 days.
On Wednesday Christopher Hill, the US chief nuclear negotiator, said in Beijing he was optimistic about making progress in talks with his North Korean counterpart on resolving "technical issues".
"We have an understanding on what needs to be done [for disabling], so there's just some issues subject to technical matters," he said.
|Hill was optimistic about making progress in|
talks with North Korea [Reuters]
"We are not in that situation where we want to do more and they want to do less. We are beyond that."
Hill said he will also be meeting Chinese and Russian officials.
North Korea agreed to disable the main parts of its Yongbyon complex by the end of the year following six-party talks involving North and South Korea, the US, Japan, Russia and host China.
Pyongyang also agreed to fully disclose all its atomic activities by December.
The US experts will conduct about 10 disablement measures on the main reactor, the reprocessing plant and the fuel fabrication plant at Yongbyon.
'Process to abandon'
In Seoul, Song said once the disablement is complete it would take North Korea "a considerable period of time to restart the facilities".
Comparing the disablement process to the initial stages of scrapping a car, he said the disablement of the nuclear facilities meant "we are already in a process to abandon them".
"The agreement certainly means the denuclearisation process is moving on the right track"Lim Sung-Nam, South Korean chief envoy
The six parties to the nuclear pact will meet again later this year to discuss post-disablement steps, added Song.
At Tuesday's six-nation talks in the border village of Panmunjom, North Korea agreed to accept half the promised energy aid in the form of equipment needed to repair its decrepit power plants.
Lim Sung-Nam, South Korea's chief negotiator, said the North will receive energy-related equipment and other items such as steel.
The agreement helped clear the way for Pyongyang to start disabling its plutonium-producing plants, possibly as early as this week.
The Yonhap news agency quoted Lim as saying: "The agreement will still have to be approved by the heads of delegations meeting at the six-party talks, but it certainly means the denuclearisation process is moving on the right track."