Mohamed ElBaradei said the process of shutting the Yongbyon reactor was "a good step in the right direction".
The move is part of an deal agreed in February, in which Pyongyang pledged to disarm in exchange for fuel aid.
Analysts say that while the shutdown is important, it is just one stage in a long process to disable the reactor.
Speaking in the Thai capital, Bangkok, Mr ElBaradei said his 10-man team of experts - who arrived in North Korea on Saturday - had verified an earlier statement from Pyongyang confirming the shutdown.
"Our inspectors are there. They verified the shutting down of the reactor yesterday," he said.
The IAEA chief said that the next step was to verify the shutdown of other nuclear facilities and then disable them, something he warned would be "a complicated process".
"It's a very important step that we are taking this week, but it's a long way to go," Reuters news agency quoted him as saying.
Under the terms of the disarmament agreement, struck in February after intense negotiations, Pyongyang is to receive 50,000 tons of fuel aid for shutting Yongbyon down, and another 950,000 tons for disabling all its nuclear facilities.
Last week it received its first shipment of fuel aid, and early on Monday a second shipment was dispatched, carrying 7,500 tons of fuel from South Korea's Ulsan port, bound for Nampo in North Korea.
Talks between representatives from the six countries involved in the deal - North Korea, Japan, China, Russia, the US and South Korea - are to resume this week in the Chinese capital, Beijing.
While the news of the shutdown is bound to be welcomed by the delegates at the talks, analysts know there is a long road ahead.
In the next phase, North Korea will need to declare all the nuclear material it already has, and confirm whether it has a uranium programme in addition to the plutonium produced at Yongbyon, correspondents say.Persuading North Korea to disable the reactor completely, or give up any nuclear weapons it already has, may prove far more difficult than the initial shutdown, according to the BBC's Kevin Kim in Seoul.