SYDNEY (AFP) - Australia ordered an investigation on Wednesday into how an asylum-seeker boat managed to reach one of the country's busiest ports undetected and warned that those on board may be flown back home.

The rickety vessel carrying 66 Sri Lankans was spotted on Tuesday within the harbour limits of Geraldton in Western Australia, 425km north of Perth.

The state's Premier Colin Barnett called it "a serious, unprecedented and unacceptable breach of Australia's border security" - the first such boat to reach the Australian mainland in five years.

Home Affairs Minister Jason Clare said most vessels opted for the shortest route to Australia, which took them to the country's Indian Ocean territory of Christmas Island, 2,000km to the north-west of Geraldton.

He told ABC that radio border protection authorities had advised him the boat made an unusual, and much longer journey.

"Their initial advice is they believe the vessel travelled directly from Sri Lanka to Geraldton, which meant that it travelled in a way that is south of the main surveillance area, south of where most of our planes and patrol boats are focused," he said.

"All of our patrol boats and our surveillance aircraft are targeted at the north-west where 99 per cent of vessels arrive and are intercepted.

"I've asked customs and border protection to review the circumstances of this case and advise me whether there needs to be changes to the way in which we patrol the seas in the north-west," he added.

Reports said the boat was attempting to get to New Zealand.

Australia has in recent months flown home hundreds of Sri Lankans who failed to meet refugee requirements and Mr Clare said these rules would also apply to the Geraldton boatload.

"If these people don't meet the refugee requirements then they'll be flown back to Sri Lanka," he said.

"It's the most effective thing we've been able to do in the last few months."

Australia is facing a steady influx of asylum-seekers arriving by boat, many of whom use Indonesia as a transit hub. They pay people-smugglers for passage on leaky wooden vessels after fleeing their home countries.

It is an inflammatory political issue in Australia and certain to dominate national elections due in September, despite the fact that overall arrival numbers are relatively low by global standards.