Arise Church, which was last year hit by accusations of sexual misconduct, overworking members and racism, was given a tent at the annual event by Otago University Students Association (OUSA).
The church's contract with OUSA was cancelled following complaints about the church's presence yesterday and it was not present at the Museum Reserve today.
OUSA has acknowledged it was a mistake to allow the church to push for new members at the annual event, saying it was an "unfortunate oversight".
In an email to a student who complained, OUSA president Quintin Jane said the contract with the church was organised by an employee who was unaware of the scandal associated with the church.
"Giving them the contract was an unfortunate oversight in the first place, and if I'd been aware of this sooner I would've asked that this was cancelled before they were ever here.
"We're doing work at the moment to ensure nothing like this will happen again, and arise will not be at future tent cities."
Postgrad University of Otago student Jordan Dougherty said it was concerning OUSA gave the church a tent.
"Yesterday I was walking through Tent City and saw that Arise Church had a tent.
"This is super-concerning following the investigations and news last year about how the church harassed, took advantage of and abused unpaid interns on multiple occasions.
"It’s dangerous to have known predatory groups engaging with new and returning students in a way that implies they are sanctioned by OUSA and the university."
In a statement provided to the Otago Daily Times, Mr Jane said the OUSA extended Arise's suspension as a member of its clubs and societies.
"This action then questioned their attendance at Tent City for Ori 23.
"After internal discussion, it was decided, in line with the extended suspension, that they would be removed from any further participation in Tent City."
He said OUSA continued to be in conversation with Arise.
An investigation into the church last year heard allegations of cult-like behaviour, sexual harrassment, racism a lack of financial transparency, and members being actively discouraged taking complaints to police.
Former members of Arise Church also alleged a naked pastor chased a churchgoer in Dunedin and that interns were mistreated on tour.
Former churchgoers alleged Brent Cameron, pastor and brother of the church's founder John Cameron, was notorious for getting naked in front of interns, labelling them with derogatory nicknames, and boasting to his colleagues about his behaviour.
