Huang Jiefu, who was trained in Sydney and until recently China's vice-minister for health, today oversees Beijing's organ transplant committee.
The university awarded Huang an honorary professorship that was recently extended for another three years, sparking an outcry.
Sydney professor of medicine Maria Fiatarone Singh is organising a petition to have Huang's honours overturned.
In an open letter, Singh said Chinese officials used execution by lethal injection as a way to take and preserve prisoners' organs.
Huang, a liver transplant surgeon, and the Beijing government had paid only "lip service" to stopping organ harvesting from prisoners, she said.
"They are basically still practising execution on demand."
Signatories of the petition include medical professionals from the United States, Germany and Israel.
"The person is anaesthetised, they don't die straight away, (that) gives the surgeons time to take out as many organs as they would like to, and then the lethal injection finalised," Singh said.
China insists that prisoners and their families give consent for their organs to be used but the United Nations and the World Health Organization have condemned the practice.
China executes about 4,000 a year, human rights groups say.
Greens party MP David Shoebridge told the Australian Broadcasting Corporation: "One of our most prestigious institutions, the University of Sydney, is meant to be standing up for the best ideal of society, democracy, academic freedom."
"For it to be awarding some of its highest honours to a medical practitioner who benefited, year after year, from transplanting the organs of executed prisoners, is a betrayal of those key ideals."
Human rights lawyer David Matas branded Huang unethical.
"Huang Jiefu, being responsible for an unethical system, and himself participating in transplants, has engaged in unethical behaviour and his professorship should be revoked," he said.
However, University of Sydney transplant surgery professor Richard Allen said that in the global transplant community Huang is "an absolute champion and a hero" for his reform efforts.
Huang in 2005 became China's first senior government health official to openly admit that transplant patients received organs harvested from condemned criminals.
China has said it will begin to phase out the use of executed prisoners as a source of organs for transplants this year.
The university's medical school dean Bruce Robinson supported Huang's appointment to honorary professor.
"We believe this is a very, very important set of principles that Jeifu is pursuing in China, and that is reform of use of transplanted organs," Robinson said.