The state counsellor of Burma studied at St Hugh’s College between 1964 and 1967, earning a BA in Philosophy, Politics and Economics.
The Swan student newspaper reported the painting was taken down on Thursday and replaced with a painting by Yoshihiro Takada.
It quoted Benjamin Jones from the college as saying the portrait has been moved to a “secure location” while the Takada piece was displayed “for a period”.
Aung San Suu Kyi has recently been pressed to take urgent action to end the suffering of the Muslim Rohingya people in Burma.
More than 400,000 Rohingya have fled to Bangladesh amid reports of atrocities in Rakhine at the hands of the Burmese military.
At a meeting in Naypyidaw with the Nobel Prize winner, Foreign Minister Mark Field said the violence needs to stop and called for the government to allow full humanitarian access for aid.
Ms Suu Kyi, whose position as state counsellor does not give her authority over the military, has faced international criticism for her failure to speak out against alleged human rights abuses including mass killings, gang rapes and the burning of villages.
Foreign Secretary Boris Johnson has called on Ms Suu Kyi to “show the leadership she is capable of to try to heal that terrible situation”.