JAPAN has confirmed it plans to use some of the public funds earmarked for quake and tsunami reconstruction to boost security for its controversial annual whale hunt.

Greenpeace alleged that Tokyo was siphoning money from disaster victims by spending an extra 2.28 billion yen ($A29 million) on beefed-up security for its whaling fleet. Environmental groups are expected to renew their battle with the Japanese ships soon.

Japan's whaling fleet left port yesterday for this season's annual hunt in Antarctica. The coastguard said earlier that it would deploy an unspecified number of guards to protect the ships from anti-whaling activists.

Fisheries Agency official Tatsuya Nakaoku said the extra security was designed to ensure safer hunts, and ultimately help coastal towns that are largely rely on whaling as they recover from the March 11 disasters.

"The government will support the reconstruction effort of a whaling town and nearby areas," he told AFP today.

"This program can help it reconstruct food-processing plants there... Many people in the area eat whale meat, too. They are waiting for Japan's commercial whaling to resume."

In February, Japan cut short 2010-2011 hunt by one month after bagging only one-fifth of its planned catch. It blamed interference from the US-based environmental group Sea Shepherd.

Last month, Japan passed a 12.1 trillion-yen extra budget, the third this year, to finance reconstruction and revive an economy that is still reeling from the impact of the March 11 earthquake and tsunami.

About 498.9 billion yen was earmarked for fisheries-related spending, including 2.28 billion yen for "stabilising whaling research".

"We will bolster measures against acts of sabotage by anti-whaling groups so as to stably carry out the Antarctic whaling research," the fisheries department said after the budget was passed.

Commercial whaling is banned under an international treaty but since 1987 Japan has used a loophole to carry out "lethal research" on the creatures in the name of science.

Japan says it is necessary to substantiate its view that there is a robust whale population in the world, but does not hide the fact that whale meat from this research ends up on dinner tables and in restaurants.

Anti-whaling nations and environmentalist groups routinely condemn the activity as a cover for commercial whaling.