Japanese officials said the 8,000-ton Nisshin Maru - left without engine power and carrying hundreds of thousands of litres of oil - posed no environmental threat.
Other ships from the whaling fleet have been helping to stabilise the ship and fight the blaze, which broke out yesterday and has left a crewman missing, presumed dead.
Greenpeace had said it was willing to send its ship the Esperanza - in the Southern Ocean to try to stop the whale hunt - to help.
The expedition's leader, Karli Thomas, said: "Our first thoughts are for the missing crewman and the rest of the people on board. This is not a time to play politics."
But Glenn Inwood, a spokesman for the Institute of Cetacean Research which runs Japan's whaling programme, told the Associated Press news agency: "The whole Greenpeace offer is a red herring. Their assistance is not required and will not be accepted."
A spokesman for the Japanese fisheries agency said Greenpeace had not been in touch, though the Nisshin Maru might have refused help because the ship was boarded by Greenpeace activists in New Caledonia in 1998.
The Nisshin Maru has been lashed between two other ships to stop it drifting ice while crew members fight to contain the fire below deck.
A spokesman for New Zealand's maritime agency told Reuters reporters that fears of an oil or chemical spillwere had eased after the crew managed to pump away excess water and correct the list to the ship.
It is not yet known whether the vessel will be able to restart its engines. It has been wallowing without power, less than 100 miles from the world's largest Adelie penguin colony, in an area known for stormy weather.
Anti-whaling activists have not been linked with the fire, which could put an end to the whaling season if the ship remains inoperable.
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