A group of asylum seekers who sailed into Geraldton in Western Australia yesterday are waiting to be transferred more than 2,000 kilometres north to Christmas Island.

The 66 Sri Lankan nationals arrived by boat at Geraldton Harbour yesterday afternoon, after being intercepted just 100 metres offshore when locals alerted authorities.

Geraldton is 2,240 kilometres south of Christmas Island, the usual destination of asylum seekers heading for Australia.

They spent much of the night at a facility within the Geraldton port undergoing health and security checks before buses arrived to transport the single men in the group to the Northam Detention Centre, 460 kilometres south-east of Geraldton, and the women and children to a facility in Perth.

The Immigration Department said all 66 asylum seekers would be processed at Christmas Island, but it would not say when they are due to fly there.

Lawyer David Manne from the Refugee and Immigration Legal Centre said the group had different legal rights to other asylum seekers because they landed on the Australian mainland.

Mr Mann told the ABC they could avoid being sent offshore by applying for refugee status.

"If they apply for refugee protection in Australia, under Australian due legal process, they're entitled to have their claims assessed here and to not be sent elsewhere," he said.

The Refugee Action Collective's Ian Rintoul says it is a waste of time and resources sending the asylum seekers to Christmas Island for processing.

"It's a pointless exercise, but the Government thinks there is somehow some domestic political advantage to do that," he said.

"The Government itself committed many years ago to detention being a last resort, but it's in instances like this where we find that those intentions are mostly violated in the negative.

"Rather than detention being a last resort, it's most likely in this case it's going to be a first resort."

'Didn't see it come in'

ABC Geraldton reporter Sarah Taillier saw the asylum seekers arrive yesterday:

Samantha Maisey was working at a nearby restaurant, and said the boat arrival took her by surprise.

"We didn't really see it come in. We just sort of looked up it and it was there. It had a little flag sticking up on the top and lots of people on it," she said.

Steve Branch, who manages a nearby cafe, also witnessed the boat arrive.

"There was a rickety old looking wooden boat in the harbour probably about 100 metres offshore that'd anchored there," he said.

"A lot of people on it. You could see it was quite crowded on the decks. It basically just came into the harbour, dropped anchor and waited there."

'Serious lapse'

WA Premier Colin Barnett has described the incident as a "serious, unprecedented and unacceptable breach of Australia's border security".

"It's a serious lapse and I simply cannot imagine how this could have occurred," he said.

"For a boat, in broad daylight, to have sailed onto the Australian mainland, in the south of the state and just blatantly sail into Geraldton, that is extraordinary.

"I think there needs to be some questions answered about that.

"I think the immediate issue though is to make sure people are well cared for, that there's no health risk or safety risk to the local community. I'm assured that's being handled well and is in control."

Geraldton mayor Ian Carpenter says he is unaware of an asylum boat ever reaching Geraldton before.

"I'm certainly surprised because, as you would know, I think most of these cases of these vessels come ashore around Ashmore Reef, Broome, in that general area," he said.

"We're some 2,000 kilometres south of there so it is surprising."

Opposition Immigration spokesman Scott Morrison says the "unusual sight" for Geraldton locals is further proof the Government's border protection policies are failing.

"The Government's border failures have got to the point where people just think they can turn up anywhere along the Australian coast," he said.