A cruise ship is stuck outside Sydney Heads because of a massive swell, and may be unable to enter Sydney Harbour for the next 48 hours.

The Sydney Harbour pilot has been unable to board the Carnival Spirit, said a spokeswoman for Carnival Cruise Line Australia.

The Carnival Spirit, carrying 2,500 guests, is returning from a 12-night cruise to New Caledonia, Vanuatu and Fiji.

Passengers were due to disembark the ship this morning but the large swell has prevented the ship from entering the harbour.

The ship may be close to port, but it could be a while until the passengers touch dry land, after Port Authority of NSW confirmed Sydney Harbour will remain closed for cruise ships throughout the evening due to severe weather.

Carnival Cruise Line Australia wrote on Facebook: "The Port Authority advised the earliest the Carnival Spirit could be alongside the Overseas Passenger Terminal in Circular Quay is tomorrow [Wednesday] morning".

A passenger from Sydney who is on Carnival Spirit said the waves on the coast were massive.

"It's not pleasant, it's been like this all night," she told ABC radio over the phone from the ship.

"I don't think many people got much sleep," Debbie from Cherrybrook said.

Sydney Harbour master Captain Philip Holliday said he was hopeful the Carnival Spirit could be brought safely into the harbour within 48 hours.

"We are, of course, in the hands of the gods," he said.

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"As soon as the weather improves, we'll get the pilot on board and we'll bring the ship in."

"I've been the harbour master here for almost four years and this is the first time I've closed the port and this is the first time I've ever refused entry to a cruise ship.

"The master of the ship I'm sure will be doing his best to keep the passengers as comfortable as possible ... they might spill their soup but I'm sure they'll be relatively comfortable.

"They're much better off there then trying to get the ship in when the conditions are so bad that it's too risky."

Sydney ferries have also been affected by the wild weather over the past two days.

A Sydney Ferries spokeswoman said the Manly to Circular Quay service had been suspended due to adverse weather conditions.

Ferries on Parramatta River are starting and terminating at Meadowbank due to severe tides at Rydalmere and overflowing at Parramatta Weir, she said.

Big wet closes commercial ports across NSW

Dangerous conditions have also forced the closure of Sydney Harbour and every commercial port across New South Wales for at least 24 hours, Captain Holliday said.

"The weather is rolling right through the heads at Sydney Harbour, and that's pretty rare," he said.

"Outside of the heads, we're recording swells of around 13 metres which is pretty severe.

"But even coming in through the heads we're still getting eight metres or so."

He said all commercial ports in NSW, including Eden, Yamba, Port Kembla, Newcastle, Sydney and Port Botany, were closed as ships queued to get in.

"In Port Botany, we've got five ships at the container terminal at the moment that are unable to continue cargo operations and therefore they can't sail," he said.

"We've got about eight ships waiting to come into the harbour as soon as there is space and the weather allows."

AAP/ABC