"(North Korea) ignored repeated warnings by the international community and forcibly conducted a nuclear test. It is absolutely unacceptable," Prime Minister Shinzo Abe told reporters.
"Whether we can stop North Korea's reckless actions that threaten world peace depends on the cooperation and solidarity of the international community," he added.
North Korea 'explosion' points to nuclear test
The North described the test of what it called a hydrogen bomb as a "perfect success".
In an earlier statement, Abe described North Korea's nuclear and missile programme as an increasingly "grave and urgent" threat to the safety of Japan.
"Our country lodges a strict protest against North Korea and condemns it in the strongest words," he said in the statement.
The explosion came just hours after Pyongyang claimed to have developed a hydrogen bomb that could be loaded onto a long-range missile, and after Abe held telephone talks with US President Donald Trump on the North's weapons programmes.
Japan confirms North Korea has conducted 6th nuclear test
"The government confirms that North Korea conducted a nuclear test after examining information from the weather agency and other information," Japanese Foreign Minister Taro Kono told reporters.
Defence Minister Itsunori Onodera said the ministry has begun flying "sniffer" planes capable of detecting radioactive fallout.
"We'll do our best to collect information," he said, according to public broadcaster NHK.
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