Health authorities in New South Wales have defended a decision to disrupt the travel plans of thousands of cruise ship passengers over a swine flu scare.

Almost 2,000 passengers and 900 crew onboard the Dawn Princess arrived back in Sydney on Saturday morning after a 35-day Pacific cruise.

When NSW Health learned that two of the passengers had been sick but recovered from the flu, passengers and crew were confined to the ship for up to six hours while four travellers were screened.

Queensland man Gil Harvey was one passenger forced to wait to disembark.

"Some of them are terribly annoyed," he said.

"They had flights to catch and appointments made. It's just been blown out of the water."

All of the passengers were advised to stay in Sydney overnight while swine flu tests were carried out.

NSW chief health officer Kerry Chant says it was a necessary precaution.

"We obviously consider the consequences of any public health measures we do, but in this case we felt this action was warranted," he said.

"The staff, the medical staff and the crew have been very vigilant in the way they've managed this situation.

"Assessing the information we had to hand, we felt that the actions were prudent and taking a cautionary approach and warranted in this circumstance."

Federal Health Minister Nicola Roxon says authorities were right to quarantine the cruise ship.

She has told Channel Nine the Government is doing everything it can to minimise the spread of swine flu.

"I think it is necessary for us to take all the precautionary steps that we can, particularly while this disease is not yet widespread in Australia," she said.

"That's why we are taking the steps that we are. Luckily the testing has got a lot quicker, although that was an inconvenience for several hours for people."

All four passengers were cleared of swine flu last night.

Currently the number of confirmed cases of swine flu across Australia stands at 14.