Earlier reports said the royal, who is married to Australian-born Princess Mary, was turned away from the bar under new Queensland laws that require ID scanning.
Aimed at curbing alcohol and drug-fuelled violence, the new laws require venues open past midnight in Queensland's safe-night precincts to scan IDs after 10:00pm.
Asked whether it was a "lie" that the future king of Denmark was challenged and not allowed into the nightclub because he could not prove who he was, Mr Stewart said: "No, no, that is not correct — I am not saying it is a lie — what I am saying is it is just not correct."
Mr Stewart said the visiting royal was never refused entry and the identification issue was resolved during two earlier meetings involving the Prince's entourage.
"The Prince at no time was party to those conversations and wasn't even present when the security personnel made those arrangements," he said.
"Subsequent to that, the Prince and his security detail arrived at the premises and they were facilitated into the premises where I understand the Prince enjoyed his time and left without incident."
Mr Stewart said Queensland's lockout laws had not caused an "international embarrassment".
"No, if there has been any embarrassment sadly it has been misinformation that is now in the public view," he said.
"His Royal Highness is not an internationally protected person, but it is my understanding because of his status as a visiting royal they are given special consideration in relation to their security, but also the security of our community.
"Our officers who were part of the security detail simply followed normal protocol in ensuring his safety, the safety of the Queensland public, and the enjoyment of everyone on that particular evening."
Club security needed to be sure who group were
There is CCTV vision of the negotiations at the bar's main entrance, but Jade Buddha co-owner Phil Hogan said he did not want to release it for legal reasons.
Mr Hogan said the club's security needed to be sure who the group were.
"Their first concern was — they're dealing with plain-clothes guys with guns and someone they don't recognise," he said.
"They could have been terrorists, so their first priority as security is to protect the room."
The head police officer showed his card, it was photographed, and sent to the co-owner, but Prince Frederik was still not identified.
"So now we were concerned we'd now be breaking the law in front of six police officers," he said.
After finally gaining entry, Prince Frederik broke away from the security detail and fronted up to the bar on his own.
Mr Hogan said the barman, again not recognising the royal, asked him what he wanted, to which Prince Frederik replied: "I'll have a Dark and Stormy."
Prince Frederik was reportedly in Brisbane ahead of the Hamilton Island Race Week yachting regatta.