Japan has begun injecting new tax-payer-funded subsidies into its whaling program in a bid to keep the fleet afloat, the ABC has learned.

It is believed the "profitable fisheries program" is helping to keep the so-called scientific research program's ongoing debts at bay and to help refit the whaling fleet's flagship.

With the Japanese fleet now entering Antarctic waters, the annual whale wars are again expected to flare any day.

Militant Sea Shepherd activists have been able to all but scupper the fleet's catch over the past few years.

This, plus lower demand for whale meat, means the government has been forced to prop up the whaling program.

Some of the money has come from funds set aside for the rebuilding of communities shattered by the 2011 tsunami.

And now it appears more cash has come from the new taxpayer-funded subsidy.

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"This subsidy is supposed to help fishermen in financial trouble," investigative journalist Junko Sakuma said.

"Now it's propping up the unprofitable whaling fleet, and if they keep running a loss, they won't even have to pay it back."

Documents seen by the ABC suggest the subsidy has already been used to partly refit the whaling fleet's mother ship, the Nisshin Maru, with a smoking room and internet connections.

Patrick Ramage is the whale program director at the International Fund for Animal Welfare.

Tomorrow he will release a report into just how the Japanese whaling industry is propped up financially.

"The most important finding of this new report is really three things: first, that whaling is an economic loser in the 21st century, second, that the Japanese people have lost their appetite for whale meat, and third that whale watching rather than whale killing is the economically beneficial whale industry for the 21st century," he said.

Even the strongest supporters of whaling in Japan are pessimistic about the future of the hunt, especially with the government forced to pump in more subsidies into the fleet to keep it afloat.

Masayuki Komatsu is a former Japanese delegate to the International Whaling Commission and one of the architects of the country's scientific research program.

He warns that the injection of this new subsidy is a sign that program is in big trouble.

"It's not sustainable, right. How long can you get such money from the government? Everybody likes money, particularly other people's money," he said.