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An email from the university was sent to students on Friday about the situation.
The email said both cases are linked to the World Hereford Conference in Queenstown, which took place from March 9 to March 13.
The Ministry of Health tonight released figures regarding cluster cases, including the conference.
There are now 17 confirmed cases linked to the event and one probable.
Another two people from overseas, who had been at the conference, were previously revealed to have tested positive.
Authorities are busy tracking close contacts linked to the event.
University spokeswoman Brenda Mills would not answer questions from starnews.co.nz but said a statement will be released on Saturday morning.
Said the email: "Lincoln University has confirmed that one of its students has tested positive for Covid-19.
"On Wednesday the University also confirmed that another of its students was at probable risk of having the virus."
Both students entered self-isolation on March 21.
The email asked staff and students who attended various lectures, labs or tutorials or meetings on campus, lived in the halls and dined in the main dining area between March 16-20, or attended the Queenstown conference, to self-isolate.
- Additional reporting: Angus Hilliard