In a move to reduce regional tensions, Pyongyang later said the site had been dismantled.
Reporters said they witnessed a huge blast.
North Korea’s move is seen as part of a diplomatic rapprochement with South Korea and the US.
However, scientists believe it partially collapsed after the last test in September 2017, rendering it unusable.
Independent inspectors were not allowed to witness the process of the dismantling of the Punggye-ri site in the mountainous region of the country.
The move comes ahead of a planned summit between President Donald Trump and North Korean leader Kim Jong-un in Singapore on June 12.
However, in recent days both countries have said the meeting could be delayed or even called off, amid sharp verbal exchanges between US and North Korean officials.
Three tunnels were collapsed in a series of explosions in front of about 20 handpicked international journalists.
Two blasts were reportedly carried out in the morning, and four in the afternoon.
South Korea welcomed the news.
“[We] expect it to serve as a chance for complete denuclearization going forward,” Foreign Affairs Ministry spokesman Noh Kyu-duk was quoted as saying by Yonhap news agency.
North Korea has conducted six nuclear tests since 2006 in a system of tunnels dug below Mount Mantap.
It is thought to have been the country’s main nuclear facility and until now the only active nuclear testing site in the world.
The facility is located about 230 miles north-east of Pyongyang.
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