Japan has refused to provide its share of the 1 million tons of fuel aid pledged to the reclusive communist state, demanding that Pyongyang first disclose all information on Japanese nationals abducted by the North during the 1970s and 1980s.
In response, North Korea has called for Japan to be excluded from the six-party negotiations, which also include Russia, South Korea, the United States and China.
Tokyo has also opposed Washington's decision to remove Pyongyang from its terrorism blacklist, announced on October 11 after a deal was reached with North Korea on verifying its past nuclear activities.
"Japan should play a greater role in the denuclearization of the Korean Peninsula," said Kim Sook, South Korea's chief negotiator and deputy foreign minister, after a meeting with his Russian counterpart, Alexei Borodavkin.
"However, it would be undesirable to go as far as to exclude Japan from the six-party negotiations," he said.
Under a February 2007 deal the North pledged to dismantle its plutonium-producing Yongbyon reactor and provide full information on its nuclear program.
Last week the UN nuclear watchdog, the International Atomic Energy Agency, said the North had resumed work to deconstruct the reactor, after a pause of several months.
Japan's position has come as a blow to the United States, which had hoped to conclude the current stage of North Korea's denuclearization process before President George Bush leaves office in January.
Various international media reports have said China, Russia, the United States and South Korea may approach another partner - possibly the European Union or Australia - to take Japan's place as a donor to North Korea.