Papua New Guinea appears set to grant Bougainville independence by June next year after their respective leaders discussed the details over a series of joint supervisory body meetings last week.

However Prime Minister James Marape conceded only the national parliament will deliberate the autonomous region's future, despite more than 98 per cent of Bougainville's electorate voting in favour of independence during a non-binding referendum in 2019.

A peace agreement in 2001 following the end of a decade-long civil war only three years earlier, which was sparked by the exploitation of the region's cooper ore mine, creating the Autonomous Bougainville Government for the east island region.

The next step requires speakers and respective clerks from both PNG and Bougainville's parliaments to establish a secessional order to map out a formal process on the road to ratifying full independence from the region's current autonomy.

"We are in the final leg in which the referendum result will go to parliament," Mr Marape said in a press conference on Friday.

"We put a clear roadmap for the first six months of next year.

"The technical specifications of the secessional order as well as what happens on the floor of parliament will be defined properly in the next three months.

"We anticipate that before the first half of 2026 has lapsed, parliament - possibly in its second sitting - would receive and deliberate on the result."

Recent talks held in Port Moresby between Bougainville President Ishmael Toroama and Mr Marape established a parliamentary bipartisan committee whose findings will assist the final deliberation of MPs for independence.

Established in New Zealand in June, the governments have been adhering to the Melanesian Agreement "to craft and pursue a clear political pathway forward" based on the referendum result as an extension of the Bougainville Peace Agreement.

However political figures in PNG, including from the autonomous region, appear uncertain over what methodology will decide ratification for independence in the secessional order.

They include a simple majority vote or a two-thirds absolute majority, which is in line with constitutional amendments in the country.

Other considerations relate to whether Bougainville has the institutional and/or economy capacity to be given immediate independence, with both points raised in the supervisory meetings.

The rhetoric took place last week amid lingering tension between the Autonomous Bougainville Government and PNG's national government.

President Ishmael Toroama said the joint meetings could be rendered irrelevant when considering the growing movement in Bougainville.

He cited the example of a restoration and development fund which is intended for Bougainville - worth close to $A40 million (100 million kina) - that will only come to fruition from a sole MP sitting in the PNG national parliament.

"It is deeply concerning that in this matter, though it's initiated by the Autonomous Bougainville Government through the courts, the regional member for Bougainville and your state minister has chosen to actively defend against the implementation of joint supervisory body-endorsed decisions on this funding," Mr Toroama said.

"His public statements that the joint supervisory body resolutions do not change the law reflects a total disregard for the sanctity and constitutionality of the joint supervisory body as a legitimate body from in which the Prime Minister's commitment funds originate.

"Such actions risk undermining the joint supervisory body's authority.

"This is very dangerous and has the potential to be perilous to the peace process."