Sgt. Sean Whitcomb says the man did not have permission to be aboard the passenger ferry boat. The man was being questioned Sunday afternoon and was to be booked into King County Jail.
The boat was reported drifting about 300 yards from Pier 69 on the Seattle waterfront about 7 a.m.
Police say the U.S. Coast Guard and Seattle police were contacted when a tugboat was sent to retrieve it and a man was discovered on board.
SWAT officers eventually boarded the boat and arrested the man.
Police say the man told police he took the boat because he wanted to go to West Seattle. They're still trying to determine how he managed to commandeer the ship.
The Victoria Clipper provides ferry service between Seattle and Victoria, B.C.
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