Mr Morrison and other members of the federal government have been in direct contact with their Indonesian counterparts over Bashir's impending release.

"Australians died horrifically on that night, and I think Australians everywhere would be expecting that this matter was treated with the utmost seriousness by our government, which it is," he told reporters on Monday.

"But also that the Indonesian government would show great respect for Australia in how they manage this issue."

Bashir, 81, is considered the spiritual leader of Islamist group Jemaah Islamiah.

The radical Muslim cleric was convicted of terrorism charges in 2010 over links to militant training camps in Aceh province and jailed for 15 years.

But Indonesian President Joko Widodo has confirmed Bashir will be granted early release from jail on humanitarian grounds.

Eighty-eight of the more than 200 people killed in the 2002 bombings of Bali nightclubs were Australians, and Canberra has previously urged against leniency for Bashir.

"We have been consistent always - governments of both persuasions, over a long period of time - about our concerns about Abu Bakar Bashir," Mr Morrison said.

"He should serve what the Indonesian justice system has delivered to him as his sentence."

The prime minister said it was not uncommon for prisoners who have served two-thirds of their Indonesian prison sentences to get parole.

"But we have been very clear about the need to ensure that as part of our joint counter-terrorism efforts - we have an excellent counter-terrorism partnership with Indonesia - that Abu Bakar Bashir would not be in any position or in any way able to influence or incite anything," he said.

"Let's not forget that Bali bombing led to the deaths of Indonesians as well."

The 2002 bombings spurred Indonesia to set up an elite anti-terrorism squad that receives funds and training from Australia and the US.

Indonesian security officials have previously raised concerns about Bashir's influence in radical networks.

Australian Associated Press