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The prince and his entourage were initially denied entry to the city's Jade Buddha bar on Friday because of tough new laws requiring venues to scan the IDs of patrons arriving after 10pm.
Co-owner Phil Hogan told AAP the royal visitor was admitted after officers from Queensland Police's Dignitary Protection Unit assured him the Office of Liquor and Gaming Regulation had agreed to make an exception for the future king.
But Mr Hogan is now worried he might be fined after an OLGR spokeswoman contradicted his version of events.
The spokeswoman said the OLGR was "unaware of this incident" until Monday, while a police spokesman said it did "not discuss operational security arrangements for dignitaries".
Mr Hogan maintained "we did everything we reasonably could".
"If they're saying that police didn't contact them then that's news to us," he said.
Mr Hogan warned he had "plenty of evidence" to back up what had occurred.
The kerfuffle has reignited debate about the controversial ID scanning laws, which came into effect last month.
Premier Annastacia Palaszczuk and Attorney-General Yvette D'Ath defended the legislation in parliament on Tuesday after coming under fire from the opposition.
Ms D'Ath said she was not aware of any complaint made by the prince.
"If reports are correct the licensed venue applied the law equally to Prince Frederik as with anyone else visiting our venues," she said.
"The prince did obviously not take great offence to this as he returned a short time later and was granted entry."
Ms D'Ath said it had not caused a "diplomatic incident as some would have you believe" and Queenslanders should be pleased the law applied to everyone.
But Opposition Leader Tim Nicholls said the premier should apologise to the prince, an avid sailor who's in Australia for the Hamilton Island Race Week, for the "slap in the face".
Mr Nicholls questioned if the royal fairytale romance with his future princess bride Mary Donaldson could have happened in modern-day Brisbane because he wouldn't have been allowed inside any venue.
The couple met in a random encounter at Sydney's Slip Inn bar during the 2000 Olympics.
Ms Palaszczuk said there was "bipartisan support" for the ID scanning laws because they were backed by the LNP when it was in government.
But One Nation Queensland leader Steve Dickson told AAP he would roll back the legislation if the party held the balance of power after the next election.