Six countries, including Japan, Malaysia, Vietnam and New Zealand will be represented by ministers at the two-day summit, to be launched by Prime Minister Tony Abbott in Sydney on Thursday.
But, despite being one of Australia's key regional partners in tackling extremism, Indonesia won't be sending a minister and will instead send its ambassador to Australia Nadjib Riphat Kesoema.
Indonesia's ministerial absence suggests continuing tensions following the executions of Andrew Chan and Myuran Sukumaran in April despite the Australian government's repeated pleas for clemency.
It comes, too, after Defence Minister Kevin Andrews did not hold a bilateral meeting with his Indonesian counterpart at the recent Shangri-La Dialogue, although both attended the Asian security summit in Singapore at the end of May.
It is understood other Australian officials were not allowed to meet Indonesian delegates at the conference either, while "time constraints" prevented Department of Foreign Affairs and Trade secretary Peter Varghese meeting with his Indonesian counterpart.
After the executions, Australia took the unprecedented step of recalling ambassador Paul Grigson from Jakarta and Mr Abbott said contact between ministers had been suspended "for some time".
Mr Grigson returned to Jakarta on Monday.
But some defence cooperation has continued.
"There's some sort of lower level interaction taking place between the defence establishments of the two countries," Australian Strategic Policy Institute director Peter Jennings told AAP, adding that intelligence sharing and police co-operation had never stopped.
Meanwhile, the immigration minister has criticised what he says is scaremongering about plans to strip dual-nationality terror supporters of their Australian citizenship.
Peter Dutton made the comments while confirming those in line for deportation will be able to appeal against the decision all the way to the High Court.
Echoing the government's special envoy for citizenship, Philip Ruddock, the minister said legislation being drafted will include provisions for the process to be challenged.Mr Dutton refused to criticise Howard government minister Amanda Vanstone over her claim on Monday that having ministers strip away citizenship without an appeal was "profoundly dumb".
"I think everybody in the Howard government did a great job and I think ministers in the Abbott government are doing a great job," he said.
Ex-Liberal minister Helen Coonan also expressed concern at the process, saying the courts should play a role in assessing the merits of a case.
Labor has provided in-principle support for the idea, but wants to receive a detailed briefing on the government's plans.
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