A chartered jet flown from the Cocos Islands to Sri Lanka overnight returned the group of asylum seekers, including children, who had arrived by boat on Monday, locals say.

The arrival of the apparently undetected boat marked the first reported asylum seeker vessel to reach Australian territory in nearly two years.

One resident counted seven children in the group including babies.

He said on Thursday night he saw the group being herded from a mini-bus with covered windows onto a plane at the local airport.

"It was all done specifically under the cover of darkness," he said.

"The way they positioned the vehicles was to obscure as much as possible."

"We all live on the runway basically, it's hard to sneak a big white plane in without anyone knowing."

"There's babies in there, less than one year old. It made it a lot more human."

A local gave Hack a video they say was captured at the airport. It shows a mini-bus with covered windows and a large white passenger jet on the runway.

Skip Instagram Post FireFox NVDA users - To access the following content, press 'M' to enter the iFrame. A video posted by triplejHack (@triplejhack) on May 5, 2016 at 10:05pm PDT

Another Cocos Island resident confirmed there was at least one child in the group.

A flight tracking website showed a flight listed to depart from Cocos, but with no destination, landed in the Sri Lankan capital Colombo early this morning, according to refugee activist Jessie Taylor.

The Department of Immigration and Border Protection has refused to comment on "operational matters" and therefore won't confirm the number of people in the group.

Locals have told Hack there are between 12-25 people.

Boat anchored 'about 500m' from island

Earlier this week Hack reported a boat carrying Sri Lankan asylum seekers arrived within the Cocos Islands on Monday morning in rough weather.

The thinly populated chain of islands and coral atolls located mid-way between the mainland and Sri Lanka is a territory of Australia.

Local Awie Rasa told Hack he saw the 10-11m wooden boat coming through the passage of the entrance to the main lagoon between the two largest islands about 10:45am.

"It's moving pretty fast, moving 12-15 knots," he told Hack.

"It's heading towards Home Island."

Mr Rasa was taking a ferry from Home Island, which is the most populous, to the capital on West Island.

"When we got to West Island jetty I can see police are preparing for their job. The customs on the jetty are running up and down and getting their tenders into the water."

"I heard it didn't reach Home Island, just anchorage around about 500m away from Home Island.

"That's pretty close."

He said he had worked as a skipper escorting asylum seeker vessels until last year and he believed "the yellow and light blue" boat was Sri Lankan.

"They’ve got the same colour boat - they're all coloured the same."

He believed there were 12 people on board.

Another local man told Hack he saw the boat from shore when it was "well and truly inside the lagoon".

He said the Australian Federal Police then escorted the boat to a mooring and two Border Force launches "appeared at great speed over the horizon".

He said the suspected Sri Lankan asylum seekers were then taken to a Border Force vessel.

"We've had a significant presence [of] Navy and Customs guys for many months. They come, they go, they disappear for a few days and come back," he said.

"As far as vessels reaching the lagoon and getting inside the lagoon – that's certainly the closest one that's got in for some time."

A Border Force spokesperson said the Department would not comment on operational matters.

The last asylum seeker boat reported to arrive in Australia was a vessel of 157 people intercepted in July 2014 near Christmas Island.

The people from that vessel spent a month on a Customs ship before being transferred to the Curtin Detention Centre and then Nauru in mid-2014.