Trade Minister Simon Birmingham indicated Australia may appeal the imposition of a 73.6 per cent anti-dumping tariff and a 6.9 per cent anti-subsidy tariff slapped on all Australian barley from Tuesday.
"Australia is deeply disappointed with China's decision to impose duties on Australian barley," he said in a statement.
"We reject the basis of this decision and will be assessing the details of the findings while we consider the next steps.
"We reserve all rights to appeal this matter further and are confident that Australian farmers are among the most productive in the world, who operate without government subsidy of prices."
China's Ministry of Commerce announced the tariffs late on Monday after completing a 16-month investigation into an anti-dumping complaint.
"The investigating authority has ruled that there was dumping of imported barley from Australia and the domestic industry suffered substantial damage," a statement on the ministry's website said.
The tariffs are a huge blow to Australia's barley trade with China, which is understood to cover about half of all barley exports.
Barley producers are also deeply disappointed by the decision and rejected China's claims of dumping.
They warned it would cost the grains industry and rural and regional economies $500 million a year in lost exports.
"The tariffs are a huge blow to Australia's barley trade with China," the Grains Industry Market Access Forum, Australian Grain Exporters Council, GrainGrowers, Grain Producers Australia and Grain Trade Australia said in a joint statement.
"These tariffs will disrupt and most likely halt exports by artificially increasing the price of Australian barley imported to China until the situation is resolved."
The punitive tariffs come just one week after China imposed a ban on meat imports from four Australian processing plants.
The measures increase suspicions that China is punishing Australia for pushing for an international investigation into the COVID-19 pandemic, and particularly the source of the outbreak.
On Monday night more than 110 countries co-sponsored an Australian-backed motion for an independent international investigation at the World Health Assembly.
WHO Director-General Tedros Ghebreyesus promised an investigation before the vote went ahead, while President Xi Jinping said his country supported a "comprehensive evaluation of the global response".
"This work needs a scientific and professional attitude and needs to be led by the WHO, and the principles of objectivity and fairness need to be upheld," Xi told the summit.
Prime Minister Scott Morrison previously described the push for an inquiry into the origins of the coronavirus as completely unremarkable.
But China's Foreign Minister Wang Yi has accused foreign lawmakers of politicising the pandemic.
Beijing's ambassador in Canberra has also raised the prospect of consumer boycotts of Australian products because of the push for an inquiry.
Aside from the tensions over coronavirus, Mr Birmingham admitted that China had long-standing grievances over Australian tariffs on its steel.
"We have had representations in the past from China in relation to our anti-dumping system," he told the Australian Financial Review.
"Anti-dumping disputes shouldn't be resolved by scorecard though. They should be resolved on the merits of each individual argument."
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