The words "kill Chinese" were inscribed above a swastika in restrooms at the University of Sydney.
The university condemned the graffiti and said "any and all remnants" would be removed.
Last week, racist flyers directed at Chinese students were posted at two universities in Melbourne.
"The University of Sydney is committed to ensuring that our community is a safe, inclusive and supportive one," it said in a statement.
"Any graffiti or posters placed around campus of a racist nature are immediately removed."
A university spokesperson told SBS: "We do not know who is responsible, although the university's security people suggest that it appears to be the work of a lone individual."
Poppy Wang, vice-president of the university's Chinese Students Association, said the graffiti had made her feel less secure.
"Most people I talk to feel sad because they come to this country to study, not to be treated like this," she told the BBC.
"They really like this country and they do not really want to see this stuff happen."
Ms Wang said she was disappointed the university had taken two days to remove the graffiti, which was found in the international students' lounge and the business school.
"The university is not reacting fast enough," she said.
Last week, fake posters bearing the logos of the University of Melbourne and Monash University were found at both institutions.
The flyers read: "Attention, entry into the campus of Chinese students should be strictly prohibited. If violated, you can be deported from the country."
Both universities said the material was fabricated and unacceptable. The flyers have been reported to police.
Student Lisa Lu said on Twitter: "I don't know who would do this on the very first day of the new semester. Even [if] it's a joke IT IS NOT FUNNY AT ALL!"
University of Melbourne Union president Yan Zhuang said he "vehemently" opposed the material.
"The posters have been attributed to a white supremacist, neo-Nazi group which has previously targeted the University of Melbourne," he said.
More than a quarter of international students in Australia come from China. But the country is also home to a significant Australian-Chinese population. In the 2016 census, 5.6% of Australians said they had Chinese ancestry.
Five takeaways from Australia's census
Racist graffiti targeting Chinese students has prompted anger after it was found at two locations in an Australian university.