"This is in clear violation of numerous UN Security Council resolutions and in complete disregard of the repeated demands of the international community," said Yukiya Amano, chief of the International Atomic Energy Agency.
"It is a deeply troubling and regrettable act," Amano said in a statement.
The UN Security Council had in Resolution 2270 in March "condemned in the strongest terms" North Korea's previous test in January, Amano said.
It had reaffirmed that Pyongyang must "abandon all nuclear weapons and existing nuclear programmes in a complete, verifiable and irreversible manner, and immediately cease all related activities," he recalled.
The Vienna-based IAEA was kicked out of North Korea in 2009.
Pyongyang's state media said the latest test, which comes after a series of ballistic missile launches that have drawn international condemnation and UN sanctions, had achieved its goal of being able to fit a miniaturised nuclear warhead on a rocket.
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