Violence in Myanmar has seen more than 400,000 Rohingya Muslims flee to neighbouring Bangladesh.
Myanmar's de facto leader has been criticised for failing to address UN allegations of ethnic cleansing.
St Hugh's College said her portrait had been replaced with a Japanese painting.
t swapped the painting earlier for one by Japanese artist Yoshihiro Takada.
Communications manager Benjamin Jones told The Swan student newspaper the portrait had been moved to a "secure location" while Takada's piece was to be displayed "for a period".
The new painting was presented to the college earlier this month and is currently displayed in the entrance of the college's main building.
Ms Suu Kyi, a former political prisoner who has been Myanmar's civilian leader since winning elections in 2015, is coming under growing international pressure to act.
In a speech on Tuesday, the Nobel Prize winner condemned human rights abuses but did not blame the army or address allegations of ethnic cleansing.
She graduated from St Hugh's College in 1967 and was awarded an honorary degree in June 2012, which the university said it was not considering removing.
Founded in 1886, St Hugh's is one of the largest colleges at the university with about 800 students. It has been contacted for a comment.
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