Greenpeace says 2.3bn yen ($30m; £19m) is being used to fund extra security measures for the whaling fleet.
Japanese officials argued when they applied for extra funding that whaling helped coastal communities.
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.
Militant anti-whaling groups attack the fleet every year, and last year forced the Japanese to abandon its programme before it was completed.
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 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.