The portrait, which was on display in the main entrance of St Hugh's College, has been placed in storage and was replaced on Thursday with a new painting gifted by Japanese artist Yoshihiro Takada.
Nobel Peace Prize laureate Suu Kyi studied at St Hugh's, graduating in philosophy, politics and economics in 1967 before completing a masters in politics in 1968.
"We received a new painting earlier this month which will be exhibited at the main entrance for a period," the college said in a statement.
"The painting of Aung San Suu Kyi has meanwhile been moved to a secure location."
The university did not say whether the removal was linked to the ongoing crisis in Myanmar's western Rakhine State.
Communal violence has torn through the state since Muslim minority Rohingya militants staged deadly attacks on police posts on August 25.
The United Nations describes the situation as "ethnic cleansing".
The removal of the 1997 portrait by the Chinese artist Chen Yanning comes a few days before new students arrive at the college to start their courses.
The portrait belonged to Suu Kyi's husband, the Oxford academic Michael Aris, and was bequeathed to the college after his death in 1999.
St Hugh's also counts British Prime Minister Theresa May among its alumni.
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