A South Korean defence ministry spokesman said that "based on our analysis, we believe that the North conducted a nuclear test today".
The news intensified worries about geopolitical tensions in the region as world powers including China struggle to rein in Pyongyang's erratic behaviour.
In early trade, Seoul's KOSPI was down 1.3 per cent while a Bank of Korea decision not to cut interest rates was unable to prevent the won sinking 0.8 per cent.
Yesterday, the European Central Bank opted against fresh stimulus, with its boss Mario Draghi calling for "patience" to see the effect of vast amounts of cash already injected into the system.
While he had not been expected to announce any action, there was disappointment Draghi did not provide any forward guidance, while some analysts said the Bank was possibly planning new measures as its bond-buying programme reaches runs out of assets to buy.
Tokyo-based dealers are also concerned at the lack of movement from Japan's central bank ahead of a policy meeting later this month, despite another weak growth reading yesterday and a general malaise across the economy.
"This is only natural, of course, as monetary policy delves further into the unknown."
Japan's Nikkei ended the morning down 0.2 per cent, while Sydney and Singapore each shed 0.7 per cent. Taipei shed 1.1 per cent and there were also sharp losses in Wellington, Manila and Jakarta.
However, Hong Kong climbed 0.4 per cent to break above the 24,000 market for the first time since August last year following a better-than-expected Chinese trade report. Shanghai was flat.
Oil prices retreated after surging yesterday on the back of data showing a sharp fall in US stockpiles.
West Texas Intermediate eased 41 cents to USD 47.21 while Brent slipped 46 cents to USD 49.53. The two contracts each rose more than USD 2 yesterday.
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