In a media statement, the Crusaders acknowledged the allegations of an incident in Cape Town involving three of its players.
"Allegations have been made via social media that there was a verbal altercation between members of the public and some Crusaders players who were out getting food after the match against the Stormers in Cape Town. The original post claimed players exhibited homophobic behaviour," the statement reads.
"The three players, team management and the South African-based security advisor with them, strongly refute the socialised account of what happened. They are devastated by the allegation and the implication of homophobic behaviour."
Crusaders chief executive Colin Mansbridge said the franchise was committed to inclusivity and proud to have earned the Rainbow Tick certification. The allegations were "particularly distressing", he said.
"Given the serious nature of these allegations I will be meeting with the team management and players on their return to Christchurch, however I am confident in the account that we have received from the team and the security advisor who was present."
Crusaders media manager Chantelle Te Haara said no further comment could be made as the team was on its way back from South Africa
South African social media influencer Alexandros Paterimos posted the accusations on his Instagram and Twitter accounts overnight.
Paterimos alleged Crusaders rugby players David Havili, George Bridge and Braydon Ennor used high pitch voices, limp wrists and homophobic slurs to mock him and his friends.
He said the Crusaders players "attacked" him and friends at McDonald's on Long St in Cape Town.
"As we entered, we were met with jeering and sniggers from them," Paterimos said.
He said Bridge recorded video of the group on his phone, presumably for Instagram or Snapchat.
"They told us they did it because we looked 'funny' to them," Paterimos said.
He said the players physically intimidated him and his group of friends, when challenged over the recording.
Bridge has blocked Paterimos and made his account private following the allegations.
Comments have been disabled on the Crusaders Instagram account following the accusations.