The M/S Birka Stockholm was travelling through Furusundsleden, which connects the archipelago to the Baltic sea, when a man toppled overboard.
Emergency services were alerted to the accident just after midnight. They responded by sending several search and rescue teams while a helicopter took part in the search efforts.
Less than three hours later, however, emergency services abandoned the search for the missing man.
He is now feared dead, reported the TT news agency on Thursday morning.