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The intruders leave anything from burger wrappers to condoms on board.
Pacific Jemm skipper Blair Payne said while the issue was not a new one, he wanted those caught to be prosecuted, rather than given warnings.
Mr Payne said the boat had signs warning people to keep off ''but this seems to be more of a trophy than a deterrent because they keep getting stolen''.
On the past three occasions, people had left personal items such as wallets and cellphones on the boat.
''The fact is that a lot of people think it's tourists, but on the several occasions that we have caught people they have actually been locals, which is disappointing.''
Pacific Jemm was the owners' holiday home when they were in the resort, and ''this is breaking into a person's home and a warning doesn't cut it''.
Mr Payne said they tried winching the boat a couple of metres away from the wharf but people walked across the ropes.
About a year ago, a person fell off the boat ramp while attempting to get on the boat and suffered severe facial injuries.
In 2012, a group of young Englishmen who were caught defecating on the TSS Earnslaw were given diversion.
Southern Discoveries' Spirit of Queenstown, which is moored alongside Pacific Jemm, has also been targeted by intoxicated revellers. The boat arrived in Queenstown in August and the company's operations manager, Douglas Keith, said bottles had been thrown at the boat in the past three weeks.
Fortunately, the damage - scratches to the glass windows - was barely noticeable.
Southern Discoveries general manager John Robson said the company was at loss as to what to do. The only solution would be to close the wharf by installing a wire fence but the company was reluctant to see that happen.
''The last thing you want is to see a wire gate closing off the wharf,'' Mr Robson said.
Senior Constable Chris Blackford, of Queenstown, said a commercial boat operator in Queenstown Bay complained to police on Tuesday evening about people ''constantly'' boarding boats.
Extra police surveillance was sought. However, Snr Const Blackford said it was up to the operators ''to take some preventive measures of their own''.
The owners of The Luanda Experience and Million Dollar Cruise, also berthed at Queenstown Wharf, said it was not an issue for them.
The owner of Clearwater Fishing declined to comment.