Japan has used funds from its tsunami recovery budget to subsidise its controversial annual whaling programme, environmental activists say.
Greenpeace says 2.3bn yen ($30m; £19m) from a budget of 12.1 trillion yen is being used to fund extra security.
Japanese officials argued when they applied for extra funding that whaling helped coastal communities.
The whaling fleet reportedly headed for Antarctic waters this week, though Tokyo has not confirmed the reports.
There has been a ban on commercial whaling for 25 years, but Japan catches about 1,000 whales each year in what it says is a scientific research programme.
Critics say those claims are just a cover for a commercial operation, and accuse the Japanese of hunting the animals to the brink of extinction only for food.
Activists from the Sea Shepherd group have attacked the fleet as part of their campaign against whaling.
Last year Japanese abandoned its programme before it was completed, citing "harassment" from the group.
Earlier this year, the Japanese Fisheries Agency applied to the government for extra funding for its programme from the emergency budget aimed at helping communities recover from the devastating tsunami and earthquake.
The agency argued that some of the towns and villages affected relied on whaling for their livelihoods.
Activists say the agency's funding request was approved and it has spent the money on extra security and covering its debts.
Junichi Sato, from Greenpeace Japan, told Australia's ABC that there was no link between the whaling programme and the tsunami recovery.
"It is simply used to cover the debts of the whaling programme, because the whaling programme itself has been suffering from big financial problems," he said.
The Australian and New Zealand governments have both criticised Japan's decision to continue whaling.
They are both considering sending vessels to monitor the whaling fleet.
Sea Shepherd activists have promised to carry on their campaign against the whaling fleet.