"We go to see the facilities and continue our discussions in more details," Heinonen said as he left Pyongyang on Thursday morning for the journey to Yongbyon.
However he emphasized that the visit to Yongbyon, expected to last into Friday, was not a formal inspection.
"We are here to talk about the verification and monitoring arrangement," Heinonen said.
"The reason that the N. Koreans are so poor and hungry is because their communist government is completely inept"
Tom Dougherty, Atlanta, USA
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The IAEA team's visit to the North's main plutonium-producing reactor came as neighboring Japan responded angrily to reports of new North Korean missile tests.
Shinzo Abe, the Japanese prime minister, desribed the short-range tests as a provocation that defied the United Nations and could destabilize the region.
"We need to seek a harsh response from the international community," Abe said in Tokyo.
The tests were the third North Korean missile exercise in the past month and drew a mixed reaction from the US.
Gordon Johndroe, a White House spokesman, said the US was "deeply troubled" by the recent test-firings "during a delicate time in the six-party talks".
"We expect North Korea to refrain from conducting further provocative ballistic missile launches, activity that is destabilising to the security of northeast Asia and turn its focus to implementing its commitments under the February 13 agreement, including the immediate shut down of Yongbyon," Johndroe said.
He said North Korea's action violated a UN Security Council resolution and urged Pyongyang to refrain from further launches.
But Pentagon officials downplayed the test-firings as "routine" and "not intended to be provocative".
In 2005, North Korea announced it had atomic bombs and last year conducted its first nuclear test.
The Yongbyon complex consists of a five-megawatt reactor and a plutonium reprocessing plant, where weapons-grade material can be extracted from spent fuel rods.
The six-nation deal offered North Korea energy aid, security guarantees and better diplomatic standing in return for mothballing its nuclear programmes.
Earlier this week Pyongyang agreed to implement the plan after it was stalled for months by a dispute over some $25m in North Korean funds frozen in a Macau bank at Washington's behest.