The Viking Orion was reportedly denied permission to dock in Adelaide after authorities discovered a "marine growth" on the ship.
Australia's fisheries department said the fungus - which it called biofoul - was "potentially harmful".
Officials said the ship's hull must be cleared before entering the country.
Biofoul is an accumulation of microorganisms, plants, algae, or small animal and can allow the importation of invasive species into non-native habitats.
The fisheries department said the management of fungus was a "common practice for all arriving international vessels" and said that the ship had to be cleaned to avoid "harmful marine organisms being transported" into Australian waters.
"Professional divers were engaged directly by the vessel line/agent to clean the hull while at anchor outside Australian waters," it added.
The ship was also reportedly denied permission to dock at Christchurch, Dunedin and Hobart. One passenger wrote on Twitter that over 800 guests remained onboard, many of whom were "upset and angry" by the company's "negligence".
The 14-deck, 930-person ship - which was built in 2018 - has reportedly dropped anchor around 17 miles (27km) off the coast while the cleaning occurs.
In a statement, operator Viking admitted that a "limited amount of standard marine growth" was being cleared from the ship's hull and said that this had caused the vessel to "miss several stops on this itinerary".
But it said that it expected to sail towards the city of Melbourne in the coming hours, where it would dock on 2 January. "Viking is working directly with guests on compensation for the impact to their voyage," it added.
In a letter on Friday, the ship's captain apologised that "the current cruise falls short of your expectations" and said a member of Viking's customer relations team would make an "adjusted offer of compensation" to guests in the coming days.
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