Japanese Foreign Minister Yoriko Kawaguchi said the issue was solely between South Korea and the International Atomic Energy Agency (IAEA) and argued that it should not derail efforts to persuade Pyongyang to abandon its nuclear ambitions.
"The (nuclear experiment) matter should be handled appropriately between South Korea and the IAEA. It should be separated from the six-way nuclear talks," Kawaguchi told reporters.
The UN nuclear watchdog said Thursday it had sent inspectors to South Korea following Seoul's startling revelation that its scientists had carried out uranium enriching experiments four years ago without the government's knowledge and approval.
South Korea, for its part, said it had failed to recognize the sensitive nuclear lab experiment until it was preparing an additional report for the IAEA this year.
South Korea has a policy of keeping itself nuclear weapons-free. A row has erupted over the North's alleged drive to build atomic bombs in contravention of international agreements.
A third round of six-way talks which brought together the United States, the two Koreas, China, Japan and Russia in Beijing in an effort to resolve the impasse ended in June without tangible progress.
They agreed to meet again in the Chinese capital by the end of September for new discussions.
The stand-off over North Korea's quest for nuclear weapons erupted in October 2002 when the United States accused Pyongyang of operating a nuclear weapons program based on enriched uranium, violating the 1994 nuclear freeze of its separate plutonium producing program.