The High Court has granted a temporary reprieve to the first group of asylum seekers due to be transferred to Malaysia under the Government's people-swap deal.

The Government had been preparing to send the first group of 16 asylum seekers to Malaysia at 11:30am today.

But in a special hearing of the High Court on Sunday, Justice Kenneth Hayne ordered a temporary injunction, stopping their removal until at least 4:15pm.

Refugee lawyer David Manne, who heads the legal team involved in the case, says the injunction gives them time to argue that sending asylum seekers to Malaysia is unlawful.

He says the group fears religious persecution in Malaysia.

"All of those that we are acting for want to be able to stay in Australia, which is a signatory to the refugees convention, and to be able to have their claims for refugee protection considered here, rather than being expelled to Malaysia where they fear they would not be protected and where they fear they would face the real risk of harm," he said.

Mr Manne's team represents 40 asylum seekers, including six minors, but the temporary injunction only affects 16 men who were set to leave for Malaysia today.

The lawyers also argue that Immigration Minister Chris Bowen is the legal guardian of the unaccompanied minors in the group, and sending them to Malaysia would not be in their best interests.

Mr Manne says many of the asylum seekers are extremely fearful and distressed.

"This case is really about some very vulnerable people, asking the court whether the Australian Government has the legal power to expel them to Malaysia, where they fear that they will not be protected and they'll be at real risk of harm," he said outside the court.

A spokesman for Mr Bowen says the Government is not surprised at the legal challenge.

"No-one should doubt our resolve in this. We're committed to breaking the people smugglers' business model and deterring people from taking that very dangerous boat journey to Australia," the spokesman said.

The injunction came on the same day a boat with 50 asylum seekers on board was intercepted north-east of Christmas Island - the second to arrive since the Malaysia agreement came into effect.

'Another boat arrival'

Opposition immigration spokesman Scott Morrison says Sunday's arrival shows the Government's Malaysian people swap deal is not working.

"We have a situation where we have, once again, another boat arrival, and another example of how this Government has driven itself into a very acute policy catch-22, as they are unable to make any decision about what they will do with the fate of the children who are on board these vessels," he said.

"I mean our policy was that everyone goes to Nauru and there are no exceptions because we can provide the facilities.

"Now the Government has found itself in a position if they make one exception then that will become the rule. And that will actually encourage kids to get on boats.

"And that's why this is an ill-thought-through policy. They've led themselves in their own cul-de-sac here and whichever way they go I think the position is worse off."

Mr Bowen says nobody will doubt the Government's resolve once the arrangement is implemented.

"For this arrangement to ... have its full effect, people smugglers and asylum seekers need to see it in operation," he told Channel 10.

"Nobody will be able to doubt this Government's resolve after they have seen this arrangement implemented."

Sorry, this video has expired Government faces human rights scrutiny ( Barrie Cassidy )

However, he says the policy will not immediately deter all people smugglers.

"I've said that we should expect people smugglers to test this arrangement, of course we should," he said.

"One signature doesn't provide that sort of outcome. We have already seen some effect, we've had about 1,000 less arrivals by boat that the same period last year."

Greens Senator Sarah Hanson-Young sent her "congrats" to Mr Manne and his legal team via Twitter.

"Many Aust are shocked that the Govt is prepared to sink this low to compete with heartless policies of the Libs," she tweeted.

She had earlier made an eleventh-hour appeal to the Government to abandon plans to send asylum seeker children to Malaysia.

"We have an immigration minister who is trying to be as tough as he possibly can. Being so tough he wants to beat up on children," she said.

"Now this is a really appalling state of affairs when we see a government willing to put the lives and welfare of vulnerable children at risk simply to make a political point."

Meanwhile, residents on Christmas Island are calling on Mr Bowen to come to the island to witness the forced removal of asylum seeker children.

About 20 residents protested at the Phosphate Hill Detention Centre on Sunday.

"These people are totally disempowered by these nonsensical decisions of our Government," Christmas Island resident Kaye Bernard said.

"It happened in 2001 with the Tampa and it's about to happen again."