Some 700 Sri Lankan asylum seekers have been deported by Australia, nearly 600 of them against their will. But more than 6000 have reached Australian waters this year, and 3000 more have been caught by the Sri Lankan navy trying to leave.

All of those returned by Australia are investigated by Sri Lanka's Criminal Investigation Department. Many have been jailed.

Immigration Minister Chris Bowen said the government would continue to return people where they did not engage Australia's international obligations. ''People who pay smugglers are risking their lives and throwing their money away. There is no visa on arrival, there is no speedy outcome, and there is no special treatment.''

Nevertheless, an Afghan asylum seeker won a reprieve from deportation after the federal government lost a legal challenge. The 36-year-old man, from the Hazara ethnic minority, was granted a stay of deportation on November 24, one day before he was due to be deported to Afghanistan. The Immigration Minister unsuccessfully challenged the injunction in the Federal Court on Friday.

The Afghan, from the strife-torn Ghazni province, is the third failed asylum seeker Mr Bowen has been prevented from deporting because of pending cases before the full Federal Court. The others are another Hazara man and a Tamil asylum seeker from Sri Lanka.

The flow of boats from Sri Lanka remains solid, even increasing, despite worsening sea conditions making the trip even more perilous.

''People want to go to Australia because there is nothing for them here, no life,'' fisherman Pradeep Lusena told Fairfax Media in coastal Negombo. ''Even if they are caught and sent home, they will try again.''

Mr Lusena has relatives in jail after being deported by Australia. They are already planning another attempt.

Those wanting to come to Australia, fleeing persecution or seeking economic opportunity, have a sophisticated and expensive network of people-smugglers to turn to. The smugglers continue to promise passengers safe passage across the ocean, visas and work rights in Australia.

The reality now, however, involves long-term detention and, for some, protracted legal battles.

The Afghan man granted a reprieve arrived in Australia in 2010 claiming protection because - as a Shiite Muslim and a Hazara - he feared being persecuted or killed by the Taliban.

Federal magistrate Philip Burchardt said the man would remain in Australia until February 1, after a case with near-identical facts was decided by the full Federal Court.

That case, involving another failed Hazara asylum seeker who is referred to as SZQRB, centres on whether the court can review international treaty obligation assessments and the extent of the Immigration Minister's power to remove or allow failed asylum seekers to apply for a visa.

Earlier this month, Debbie Mortimer, SC, called Mr Bowen's decision to deport SZQRB ''irrational'' because it was made irrespective of whether earlier refugee assessments of the man were correct.

Meanwhile, two boats carrying 147 people have been intercepted off Christmas Island. Thirty-four passengers and two crew were found on board the first vessel, detected north of the island on Friday night, Border Protection Command says.

A second vessel carrying 109 passengers and two crew was detected nearby, also on Friday night. The passengers and crew have been transferred to Christmas Island to undergo security, health and identity checks.

With JANE LEE, AAP