During her time at the World Heritage site, she posed for cameras with branded shoes and sat on the Diana Seat, a marble ledge named after the late British princess who visited in 1992.
Acting on a complaint from the site's caretaker, police filed a case because any advertising or promotional work is banned at the site.
"The Miss Universe Organization would like to extend its deepest apologies to the people of India for the incident involving the reigning Miss Universe," said a statement sent to AFP late Thursday.
It said Culpo was making a video diary for fans.
"As part of these videos, we sometimes incorporate sponsors into these shoots," it said, adding the footage was not meant for commercial purposes.
"We sincerely apologise for any unintentional harm our indiscretion and insensitivity may have caused," it added.
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