"North Korea's carrying out of a nuclear test is absolutely unacceptable for Japan," Abe said in a statement on Friday, after Pyongyang conducted its fifth nuclear test, believed to be its most powerful to date.
"North Korea's nuclear development is becoming a graver threat to Japan's safety and severely undermines the peace and safety of the region and the international community," Abe said.
"Japan lodges a serious protest against North Korea and condemns it in the strongest language," he added.
The nuclear test will send tensions soaring over the North's nuclear and ballistic missile ambitions, which have already earned international condemnation and United Nations sanctions, according to AFP.
Seismic monitors detected a 5.3-magnitude "artificial earthquake" near the North's Punggye-ri nuclear test site, with "almost identical patterns" to previous detonations, South Korean experts said.