A Chinese institution that Massey University collaborates with describes itself as serving a paramilitary force which is now the target of sanctions for alleged human rights abuses in Xinjiang.
Massey has denied its links to Shihezi University constitute a direct connection to the Xinjiang Production and Construction Corps (XPCC).
The XPCC is subject to United States sanctions for alleged abuses including mass arbitrary detention and severe physical abuse.
Shihezi University's website describes the university as being based on the XPCC and adhering to its ethos.
Massey last week said Government agencies would bring its attention to any problematic activities.
“If concerns are maintained, we would comply with all guidance or instruction from the relevant government agency,” Massey said in a statement.
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However, it has emerged that the Ministry of Foreign Affairs and Trade (MFAT) has concerns about the matter.
The ministry said its concerns include what it calls credible reports of mass detentions and other large-scale human rights violations in Xinjiang.
“We would encourage all New Zealand businesses operating in Xinjiang to be conscious of these well-documented abuses and how their actions could be interpreted as an endorsement of them,” MFAT said.
But Massey has since refused to provide anyone to be interviewed on the topic, or explain how its links to Shihezi do not equate to links with the XPCC.
Before Stuff informed Massey of MFAT advice, New Zealand joined 27 other countries in June to voice concern about arbitrary detention and restrictions targeting Uyghurs and other Xinjiang minorities.
Massey last week said the Shihezi collaboration was based largely on sheep genetics, farm management and animal science.
Political analyst Dr Paul G Buchanan has said it appeared Massey wanted “official cover” for the relationship.
China has repeatedly rejected claims of widespread human rights abuses in Xinjiang, and said its policies help deter terrorism and radicalisation.
On Monday, the Chinese Communist Party newspaper China Daily said claims of forced birth control on Uyghurs were “baseless fake news” which the US and some anti-communist Western scholars concocted.
Education New Zealand (ENZ), the government agency for building international education, said Shihezi, Massey, and Peking University and Massey University signed the first Tripartite Agreement in 2005.
In May 2007, then-foreign minister Winston Peters visited Shihezi and said the agreement helped universities build on common strengths in agriculture and agricultural technology.
According to ENZ, the relationship has since expanded to include more Chinese universities and the XPCC.
John Goulter of Education New Zealand said the latest applications for the New Zealand-China Tripartite Fund were announced in May, before the US sanctions.
“ENZ administers a number of funding opportunities, including this fund, and is continually looking to reassess and improve how they are managed,” Goulter said in a statement.
“We are aware that universities do face risks that may arise from their international connections. New Zealand’s universities and the New Zealand government work collaboratively to manage these risks.”
The Ministry of Business, Innovation and Employment (MBIE) said New Zealand has an open, collaborative science system and values academic freedom.
“The government is actively seeking to increase the international connectedness of the science system,” an MBIE spokeswoman said.
“At the same time, universities do face risks that may arise from their international connections.”
MBIE said failing to mange these risks could result in loss of reputation, and damage to New Zealand's national interests.