Immigration Minister Scott Morrison says the Malaysian government has agreed to extra measures that should ultimately stop asylum seekers from reaching Australia by boat.

Mr Morrison has confirmed he visited Malaysia this week and met its home affairs minister, Dr Ahmad Zahid Hamidi.

The under-the-radar trip was confirmed at the Immigration Minister's weekly briefing on Friday.

Mr Morrison says Malaysia is a "critical geographic link in the people smugglers' chain to Australia", and he estimates more than half the asylum seekers who reach Australia transit through Malaysia.

"Disrupting arrivals at KLIA (Kuala Lumpur International Airport) or across the Thai-Malay border or preventing the passage to Sumatra across the Malacca Strait is as critical, and I would suggest even more critical, than anything we do once that boat leaves Indonesia," Mr Morrison said.

The Minister says the meeting has served to "reboot" the Australian Government's relationship with Malaysia on border protection and people smuggling.

Detainees in limbo Asylum seekers held in Darwin have told the ABC they would rather stay in detention indefinitely than be sent home to face persecution or even death. Read the story.

He says the scope of Australia's joint working group with Malaysia will be expanded beyond people smuggling alone.

"Also on issues of drugs, guns, people trafficking and other cross-border-related issues, where our border enforcement authorities have a critical role to play."

Mr Morrison says the Malaysian government has also undertaken to broaden the tighter visa arrangements that apply to Iranians entering Malaysia.

He says the rules will now be extended to Iraqi and Syrian nationals, making it harder for them to obtain visas on arrival in Kuala Lumpur, and helping to prevent Malaysia being used as a people-smuggling transit hub.

Mr Morrison also says Australia can assist in gathering intelligence that will help Malaysian authorities.

Two boats arrived in past week

Defence now runs Australia's border protection arrangements and has confirmed two boats carrying asylum seekers have arrived in the past week.

One boat was carrying 126 people, the other had 40 people on board.

Earlier this week the Government sent 28 Vietnamese nationals who arrived by boat back to Vietnam.

Defence says 10 detainees chose to return, but the rest were forced to leave Australia because they did not have a valid claim for asylum.

Stark choice presented to asylum seekers

Mr Morrison has also confirmed that the message to asylum seekers who have arrived since offshore processing was reinstated, is to return home or face indefinite detention.

In Darwin, where more than 1,000 people are living in four separate detention centres, some detainees have told the ABC they are prepared to remain locked up rather than face persecution or even death in their country of origin.

Mr Morrison says there's a stark choice.

"The choice they have is to go home or await their transfer to Nauru and Manus Island," Mr Morrison said.

"The policy is anyone who turned up after July 19, they don't come to Australia."

The Government has not provided a timeframe for when asylum seekers would be released from detention on Nauru or Manus Island.