Japan's whaling ships have returned from the Southern Ocean with their smallest catch in years, prompting the fleet's leader to blame harassment by the Sea Shepherd marine conservation group for the shortfall.

The Nisshin Maru, the fleet's mother ship, returned to Tokyo harbour yesterday with just 507 whales, a little over half the target catch of 935, according to the fisheries agency. The haul of minke whales and a single finback was well down on last year's catch of 680.

The fleet said Sea Shepherd's attempts to sabotage the hunt had deprived it of 31 days' whaling.

The annual confrontation between the two groups reached its height in January with the sinking of Sea Shepherd's high-tech powerboat, the Ady Gil, after a collision with the Shonan Maru 2 harpoon boat.

The speedboat's skipper, Peter Bethune, later boarded the Shonan Maru 2 to carry out a citizen's arrest of the captain and hand over a £2m bill for the destruction of the Ady Gil. The 45-year-old New Zealander could face a lengthy prison term after being indicted by Japanese authorities on five charges, including trespassing and assault.

The whalers used water canon and a sonic crowd control device to deter Sea Shepherd, whose crew responded by hurling rancid-butter bombs.

The whaling fleet's leader, Shigetoshi Nishiwaki, said he was "furious" with Sea Shepherd for preventing it from reaching its quota during the five-month season.

"They say they protect the sea, but they don't care about leaking oil or leaving pieces of a boat behind," he said, in a reference to the stricken Ady Gil.

This winter's catch fell one short of the total for 2006-7 season, when the fleet returned home early after a fire broke out aboard the Nissin Maru.

Japan is permitted to slaughter the whales for "scientific research" thanks to a clause in the International Whaling Commission's 1986 moratorium on commercial whaling.

As the commission prepares to meet in Morocco in June, Japan has proposed scaling back its Antarctic hunts in return for permission to step up its coastal whaling activities.

Australia, which opposes the move, has threatened to take Japan to the international court of justice unless its ends its annual hunts in the Southern Ocean, in the Antarcatic region.

The whale wars will continue in Japan with the resumption of the trial of two Greenpeace activists charged with theft and trespassing while investigating alleged embezzlement by the whaling fleet. Toru Suzuki and Junichi Sato could be sentenced to up to 10 years in prison if found guilty. A ruling is expected in June.

Greenpeace said yesterday it had called on Japanese authorities to reopen an investigation into its allegations of widespread corruption in the programme.

"Our initial allegations have been repeatedly upheld by industry insiders," Sato said. "It is time for the cover-ups, the lies, the corruption and the squandering of taxpayers' money to end."

The group said negligible demand for whale meat in Japan had created a 4,455-ton stockpile, adding that this year's catch would send another 1,800 tons into frozen storage.