Australia's Immigration Minister Scott Morrison has returned from Kuala Lumpur after striking a series of deals with Malaysia to limit the transit of asylum seekers across its territory to Indonesia.

Morrison met with Home Affairs Minister Datuk Seri Dr Ahmad Zahid Hamidi this week with agreements on "operational co-operation" under his belt.

"I was pleased to reboot our co-operation with Malaysia," he is reported by the Australian Associated Press (AAP) as telling reporters at a weekly media briefing on border protection operations on Friday.

About 60 per cent of asylum seekers transit through Malaysia to Indonesia, where they board people smuggling boats.

"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," he said.

Two important initiatives, dormant for the past year, had been restarted and upgraded, he said.

Australia will now push forward a proposed memorandum of understanding on transnational crime.

A joint Australia-Malaysia working group on people smuggling, which last met in December, will become a joint working group on transnational crime.

That is expected to provide a vehicle for joint operations and information sharing on people smuggling as well as drugs, guns and people trafficking.

Joint operations on people smuggling would start immediately.

"In addition, Dr Zahid undertook to take up our request to extend the constrained visa arrangements now in place for Iranians coming into Malaysia... to Iraqis and Syrians," he said.

Morrison said Australia's relationship with Malaysia was now in tip-top shape.

"The agreements and understandings that were built with Dr Zahid take us to a new level of co-operation. That co-operation is focused very much on operations. It's about doing things," he said.