Chinese students have provided to Fairfax Media a list of 100 names of researchers facing visa delays, along with the 16 Australian universities they had accepted offers from, and their research field.
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All of the affected PhDs are in technology and science areas, including engineering, robotics, computer science, physics, astronomy, lasers, biochemistry, microbiology and immunology.
Among the affected universities are all members of the Group of Eight, Macquarie and the University of Technology, Sydney, and RMIT and Deakin in Melbourne.
The Chinese education ministry spokesman told Fairfax Media that education was an important area of Sino-Australian exchanges.
"Every year, tens of thousands of Chinese students study in Australia. However, recently students who planned to study in Australia indeed have encountered difficulties in visa processing. The main problem is that review time is taking too long."
On Tuesday, Peter Dutton's Home Affairs department confirmed that mandatory national security checks were causing delays for 40 students who had been awarded Chinese government scholarships to participate in research in Australia. The department denied Chinese students were being targeted.
International education is Australia's third largest export industry, worth $28 billion.
One in three international students studying at Australian universities is Chinese, and the university sector has become reliant on fee-paying undergraduate and postgraduate students.
The students facing visa delays are, by contrast, scholarship recipients who have been awarded Australian and Chinese funding to undertake PhDs for either Australian qualifications or to participate in joint Australian-Chinese projects.
The Chinese ministry spokesman said: "We are negotiating with the Australian side on this matter and hope that it could be resolved properly."
In the US, Politico reported this week that the Trump administration is considering visa restrictions on Chinese science and technology graduate students wanting to study in the US, and at national laboratories, as part of its planned trade war.
Indian PhD applicants have also complained about delays in passing visa security checks in Australia.
Kirsty Needham is China Correspondent for The Sydney Morning Herald and The Age
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