The Lambeth Conference will take place at the Canterbury campus next year but now faces uncertainty, with university bosses now seeking meetings with the event organisers including Justin Welby.
While bishops attending are expected to bring their wives and husbands, earlier this year organisers confirmed those in same sex relationships wouldn't be permitted to bring their partners.
The decision by the Anglican Communion, which was made to appease conservatives within the Communion, has received criticism from MPs, some bishops and students at the University of Kent.
The US Episcopal Church said it was "concerned by the use of exclusion as a means of building communion".
The University's governing body met this week to discuss the ban after receiving a large number of concerns raised by staff, students, and members of the public, about hosting the conference.
It says it recognises the Church is permitted by law to use the ban but that it raised ethical concerns.
In a statement, the University Council said: "Members were clear that exclusion of same sex spouses, on grounds of orientation, would be contrary to the values of the University.
"Council determined that the University shall ensure that accommodation will be available on campus for those spouses affected by this decision who wish to be in Canterbury with their partners during the conference period.
"The University welcomes them and affirms its belief in, and commitment to, diversity and inclusivity."
Premier has contacted the Anglican Communion. It declined to comment.
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