"This is outrageous as the export market could lead to even more whales dying and suffering," said Claire Bass of the World Society for the Protection of Animals.
She called it a "perverse show of solidarity" between the three whaling nations and suggested Iceland could make more money from whale watching tourism than from killing whales.
In 1986 the UN convention on international trade in endangered species imposed a ban on trade in whale meat.
But Norway and Iceland have argued that whales are plentiful in the north Atlantic and do not need protection.
Loftsson estimated there were 25,000 fin whales around Iceland and 100,000 minke whales in areas where Norwegians hunt.
Iceland has not exported meat to Japan since the early 1990s.
A Norwegian official said Norway has probably not exported whale meat to Japan since just the 1986 ban.
"Now the exporters have found buyers in Japan," Halvard Johansen, deputy director general of Norway's fisheries ministry, said.
The two Nordic nations and Japan do not recognise the UN ban, saying it was a political decision.
"It was not made on scientific grounds," Johansen said.
Norway has set a quota of 1,052 whales for this season, while Iceland has set a quota of 40.
In the Antarctic, where the season ended in April, Japan caught 551 minke whales - short of a target of 850 after its hunting was disrupted by clashes with protesters.