Former Greens leader Bob Brown spearheaded the event, where protesters held signs describing the Japanese government as "bloody whale criminal".

Mr Brown accused the Australian government of being "asleep at the wheel" by not sending Environment Minister Melissa Price to the International Whaling Commission in Brazil.

Australia had sent assistant minister Anne Ruston instead who had left as talks began on Monday, local time.

Australians felt whaling was a "bloody disgrace" and Ms Ruston's absence marked the lowest ebb of government activity on the issue.

"It's been left for Brazil to take a lead at this meeting with the Australian government effectively missing in action," Mr Brown said.

In Brazil, Japan proposed an end to the decades-old ban on commercial whaling, arguing there was no longer a scientific reason for what was supposed to be a temporary measure.

"Science is clear: there are certain species of whales whose population is healthy enough to be harvested sustainably," reads the Japanese proposal.

"Japan proposes to establish a committee dedicated to sustainable whaling (including commercial whaling and aboriginal subsistence whaling)."

Japan is frustrated with the international body which it says has become "intolerant" and a "mere forum for confrontation".

If the ban on commercial whaling was lifted, it would be up to the commission to set catch limits. It's not clear when the vote will happen; the conference finishes on Friday.

But Japan faces significant opposition.

Brazil submitted a proposal that says such whaling "is no longer a necessary economic activity, has systematically reduced whale populations to dangerously low levels". The United States agrees that the ban is necessary for conservation.

Ms Ruston, speaking on the sieline's of Monday's meeting, said Australians did not believe whaling was "something that we should be undertaking in the 21st century".

"The argument that we put forward from Australia is that we don't want to see any whales killed, whether they're killed because [of] commercial whaling or whether it's so-called scientific whaling," she said.

The commission declared a "pause" to commercial whaling beginning in the 1985-1986 season, but it remains in place today. The killing of whales is allowed for research purposes, as in Japan's program, and for indigenous communities who practise subsistence hunting.

Mr Brown told the Canberra protest that whaling was a "for profit, criminal operation" subsidised by the Japanese government despite international bans and a recent $1 million fine by an Australian federal court.

The Greens wanted a full report of Ms Ruston's trip to Brazil and wanted the Australian government to send a customs vessel to patrol the Southern Ocean during the coming whaling season.

Mr Whish-Wilson said because Australia had been "weak and spineless", Japanese whalers had become bold.

Greens senators Sarah Hanson-Young and Peter Whish-Wilson said the Greens' would oppose legislation for the Trans-Pacific Partnership unless conditions were added to ban Japanese whaling.

"Why would we be signing a multilateral agreement with countries like Japan if they can't accept not only what the Australian people think about this, but international law," Senator Whish-Wilson said.

Senator Hanson-Young said the government should "muscle up".

"This is just not good enough," she said. "There's other issues [with the trade agreement]. We also know there is growing concern amongst the crossbench and Labor within the Senate as well."

The two senators also signalled they would be looking to discuss the issue with Labor and crossbench senators.

Mr Whish-Wilson said after a visit by then-prime minister Malcolm Turnbull to Japan in January, the Japanese government announced more funding for its whaling fleet.

Japanese whalers killed 120 pregnant whales last season in Antarctica's Southern Ocean, claiming it was for research purposes.

Its catch has fallen in recent years in part due to declining domestic demand for whale meat and challenges to its hunt.

Its quota is now 333, about a third the number it used to kill before the International Court of Justice ruled in 2014 that its program wasn't scientific. It revised the program and resumed the hunt in 2016.

with AP