About 27,000 people have signed a petition circulated by a conservative Catholic think tank urging the Catholic university to withdraw the invitation to Sebelius, who wrote a section of the 2010 healthcare law including a requirement employers, including most religious ones, would have to provide employees with contraception coverage.
The White House has since shifted the requirement from employers to insurance companies.
The archbishop, Cardinal Donald Wuerl, called Georgetown's invitation to Sebelius "shocking" and said university President John J. DeGioia had mischaracterized the issue by saying it was about birth control, The Washington Post reported.
DeGioia said Monday Sebelius' "presence on our campus should not be viewed as an endorsement of her views. As a Catholic and Jesuit University, Georgetown disassociates itself from any positions that are in conflict with traditional church teachings."
DeGioia "does not address the real issue for concern -- the selection of a featured speaker whose actions as a public official present the most direct challenge to religious liberty in recent history," said a statement from the Archdiocese of Washington.
Catholic bishops have said the mandated coverage for contraception violates religious freedom.