All that drew into doubt Japan's assertion that its whaling is for scientific purposes, he said.
"The court concludes that the special permits granted by Japan for the killing, taking, and treating of whales ... are not 'for purposes of scientific research'," Tomka said.
The court ordered Japan to halt any issuing of whaling permits at least until the program has been thoroughly revamped.
Japanese Foreign Affairs Ministry spokesman Noriyuki Shikata told reporters that the country "regrets and is deeply disappointed" by the decision.
But "as a state that respects the rule of law ... and as a responsible member of the global community, Japan will abide by the ruling of the court," he said.
Former Australian environment minister Peter Garrett, who helped launch the suit four years ago, said he felt vindicated by the decision.
"I'm absolutely over the moon, for all those people who wanted to see the charade of scientific whaling cease once and for all," Garrett told Australian Broadcasting Corp. radio. "I think (this) means without any shadow of a doubt that we won't see the taking of whales in the Southern Ocean in the name of science."
Although the decision is a major victory for Australia and environmental groups that oppose whaling on ethical grounds, it will not mean the end of whaling.
Japan has a second, smaller scientific program in the northern Pacific which now may also be subject to challenge. Meanwhile Norway and Iceland reject outright a 1986 moratorium on commercial whaling imposed by the International Whaling Commission.
Nevertheless, environmental groups rejoiced.
Activist Pete Bethune, a New Zealander who has clashed frequently with Japanese whalers in attempts to stop their hunt, said "justice was served" by the ruling.
"The court dissected their scientific program, pulled it to bits and it proved that the amount of science is tiny relative to the commercial aspects," he said.
He said that if Japan had prevailed, it could have led other countries to begin whaling in the Antarctic and eventually a full commercial Japanese whaling program.
Japan had argued that Australia's suit was an attempt to force its cultural norms on Japan, equivalent to Hindus demanding an international ban on killing cows.
Though consumption of whale meat has declined in popularity in Japan in recent years, it is still considered a delicacy by some. Most of the whale meat from Japanese hunts ends up being sold, though the court didn't find that that in itself makes the program commercial and not scientific.
The ruling did say explicitly that killing whales for scientific purposes would be legal under international law in the context of a better-designed study. Japan's program was supposed to determine whether commercial whaling of some species can resume without bringing them in danger of extinction.
The ruling noted among other factors that Japan had not considered a smaller program or non-lethal methods to study whale populations, and said Japan had cited only two peer-reviewed scientific papers relating to its program from 2005 to the present a period during which it has harpooned 3,600 minke whales, a handful of fin whales, and no humpback whales at all.