"We visited all the places which we are planning to visit and cooperation was excellent," Heinonen said in footage shot by APTN, adding that the facilities remain operational.
The 5-megawatt reactor, believed capable of churning out enough plutonium for one atomic bomb a year, is at the center of international efforts to halt North Korea's nuclear program. North Korea mounted its first atomic test explosion last October.
Other facilities UN officials saw at Yongbyon included an unfinished 50-megawatt reactor, the fuel fabrication plant and reprocessing plant, Heinonen said. He said he thought five facilities at the complex would likely be closed.
"North Korea is offering positive signs that it is willing to cooperate once the actual monitoring begins," said Koh Yu-hwan, a North Korea expert at Seoul's Dongguk University.
Koh, however, said the agreement between the North and the IAEA came as no surprise and was part of "necessary preparations" that have to be made before the North shuts the reactor.
In Washington, Secretary of State Condoleezza Rice said Thursday she hoped for a swift shutdown.
"We hope for now rapid progress given the beginning, we believe, of the North Korean efforts to meet their initial action obligations," Rice said, before meeting South Korean Foreign Minister Song Min-soon.
Song told reporters after the meeting that six-party nuclear talks with North Korea can resume even before the North's reactor closure is completed, as long as Pyongyang starts the shutdown, Yonhap news agency reported.
The Foreign Ministry in Seoul could not immediately confirm the comments.
Though North Korea pledged to close Yongbyon, it ignored an April deadline to do so because of a dispute with Washington over North Korean funds frozen in a Macau bank because U.S. allegations of money laundering and other wrongdoing.
That was finally settled this week after months of delays, and North Korea said Monday it would move forward with the disarmament deal.
The February agreement's initial phase calls for North Korea to shut the Yongbyon reactor and receive 50,000 tons heavy fuel oil assistance.
The showing of the Yongbyon site to the inspectors was a "well calculated" move by the North, said Paik Hak-soon, a North Korea analyst at the Sejong Institute outside Seoul.
"By allowing the IAEA delegation to visit Yongbyon, the North demonstrated to the international community its will to keep the promise to carry out the shutdown and sealing," Paik said.
But at the same time it was also a "warning to the United States" that the reactor is still running and the country could produce more plutonium unless Washington keeps its promise to give provide economic and political concessions, Paik said.