Scott Morrison has scolded the World Health Organisation for supporting the reopening of wet markets.
The prime minister said it was "unfathomable" to back live animal markets, which were likely the cause of the killer coronavirus.
"I'm totally puzzled by this decision," Mr Morrison told Nine on Tuesday.
Australia's firm stance against wildlife markets could put the country on a collision course with the global health authority.
"We need to protect the world against potential sources of outbreaks of these types of viruses," Mr Morrison said.
"It has happened too many times."
Experts believe COVID-19 originated in an exotic market in the Chinese city of Wuhan.
Health Minister Greg Hunt is also unsettled by China's plans to reopen the markets.
"There is a very real likelihood that this disease arose from a wet market in Wuhan - it's clear that these are dangerous vectors," Mr Hunt told the ABC.
"So we might disagree on this issue with some of the international authorities, but our job is to protect Australians, and I would imagine that around the world, the vast majority of people would have a similar view."
Global leaders have urged China to ban the "deadly and diseased" food markets, but the World Health Organisation disagrees.
"With adequate facilities, proper regulation and good hygiene practices it is possible to have safe food sold in wet markets," the organisation told The Australian.
Labor leader Anthony Albanese backed the prime minister's strong statements.
"We need to make sure, and China needs to make sure, that this can't happen again," he told reporters.
"So, there needs to be appropriate protections put in place. Common sense tells you that that's the case."
Australian Associated Press