Officials in New Zealand had earlier said the ship must be moved as, with over 1,000 tonnes of oil on board, it risks contaminating the world's largest Adelie penguin breeding ground, less than 200km away.
Chris Carter, New Zealand's conservation minister, said the ship was stationary in the water with "1,100 tonnes of toxic oil in it and we want it out of there".
Japan has refuted the accusations from New Zealand's government, as well as news reports, that there is a threat of pollution, calling them malevolent.
"We are grateful to Greenpeace for their offers of help, but we don't need it"
Fisheries Agency official
Greenpeace, the environmental watchdog, has made several offers to tow the ship, but Japan has rejected them, attempting instead to carry out repairs.
"We are grateful to Greenpeace for their offers of help, but we don't need it," said Moronuki.
He added that it was still too early to say where the ship might head once it can move, including whether or not it would continue its to hunt whales, in what Japan calls annual scientific research whaling.
But Karli Thomas, the Greenpeace expedition leader aboard Esperanza, the Greenpeace vessel stationed several miles from the whaler, said that time may be running out.
"If we don't get the ship out of here as soon as possible, we could see a slow-motion disaster unfolding," she said, repeating Greenpeace's offer to tow the ship.
"We feel this has been a case where the human-related issues and environmental issues have been put behind political concerns," she said.
Australian police also want to interview the crews of the two ships involved in a collision between a vessel in the Japanese whaling fleet and a ship belonging to the Sea Shepherd Conservation Society, an environmental activist group, a spokesman for the country's justice minister said on Wednesday.