"This is money that should be going to help these communities recover - not to prop up an ailing whaling operation.
"Every bit of money that's being spent on this is money the directly should have been spent on helping these communities. It's Japanese taxpayers who will be angry.
Executive director for Greenpeace Japan Junichi Sato told the Guardian the decision to pump relief funds into whaling is "downright shameful".
"It is absolutely disgraceful for the Japanese government to pump yet more taxpayer money on an unneeded, unwanted and economically unviable whaling programme, when funds are desperately needed for recovery efforts."
The Japanese fisheries agency reportedly said its use of the fund was justified because one of the towns destroyed in the March tsunami was a whaling port.
Meanwhile, New Zealand has joined several other countries in calling for the safety of those protesting whaling in the Southern Ocean.
It has joined Australia, the Netherlands and the United States jointly in condemning any actions in the Southern Ocean that could endanger human lives.
Foreign Minister Murray McCully said the four countries were deeply concerned that confrontations in the area would lead to injury or loss of life among protestors and whaling crews.
"We call on the masters of all vessels involved in these actions in the Southern Ocean to take responsibility for ensuring that safety of human life at sea is their highest priority."
Mr McCully said the countries remained firmly opposed to commercial whaling, including so-called 'scientific' whaling, particularly in the Southern Ocean Whale Sanctuary, and were disappointed by the recent departure of the Japanese whaling fleet for the Southern Ocean.
