Stewart Spence used a derogatory term about homosexuals at The Marcliffe Hotel during a Hospitality Industry Trust (HIT) Scotland event last week.
Mr Spence later said he wanted to "sincerely apologise".
VisitScotland said the Marcliffe had been removed it from its website while it investigated the incident.
The agency told the BBC that all members of its Quality Assurance Scheme scheme must comply with the Equality Act 2010.
"Scotland is an inclusive, welcoming nation, and as an organisation VisitScotland is opposed to all forms of unlawful and unfair discrimination," a spokesman said.
"VisitScotland is currently looking into this matter as a priority and in the meantime, we have suspended the Marcliffe's QA membership and the hotel's entry on VisitScotland.com."
The hotel's five-star status and website listing will not be reinstated until "written evidence" is submitted that it does not operate a discriminatory policy with staff and customers, the spokesman added.
HIT Scotland said homophobic views and comments were made about the industry during the event and that it was "shocking".
A source who was at the dinner said "jaws dropped".
Mr Spence later said in a statement: "I made some very ill-advised comments at the dinner and I am absolutely mortified.
"I would like to sincerely apologise for the offence caused. I don't know what I was thinking."
The hotel - a popular venue for wedding receptions and functions - has been at its North Deeside Road venue since 1993.
Tourism agency VisitScotland has suspended the five-star status of an Aberdeen hotel following the owner's homophobic comments.