Bougainville has voted overwhelmingly to seek independence from Papua New Guinea, with more than 97 per cent in favour of autonomy.

Key points: Some 181,067 Bougainvilleans — or 85 per cent of people enrolled — voted

Some 181,067 Bougainvilleans — or 85 per cent of people enrolled — voted Of that number, more than 170,000 voted in favour of independence

Of that number, more than 170,000 voted in favour of independence PNG and Bougainville are expected to hold negotiations to find a way forward

Out of 181,067 ballots, 176,928 votes were cast for independence.

The historic referendum was carried out over a two-week period, with people asked if they wanted independence or greater autonomy from Papua New Guinea.

The poll was a key part of a nearly 20-year-old peace agreement, which brought an end to a bloody civil war in the region.

Up to 20,000 people, or about 10 per cent of Bougainville's population, died during the Bougainville Civil War, fought from 1988 to 1998.

However, the referendum result is not binding.

Negotiations between PNG and Bougainville about the road forward will now begin and could continue for years, and the PNG Parliament will have the final say.

Bougainville Referendum Commission chair Bertie Ahern said on Tuesday the vote was conducted "in an environment that was conducive to a free, fair and credible process".

Why is the vote important?

The referendum holds huge emotional significance for many Bougainvilleans. It is the culmination of decades of work towards peace and reconciliation.

The scheduled two weeks of voting ended earlier than expected, with many Bougainvilleans casting their vote just days after polling stations opened.

Bougainville President John Momis, in a blue shirt, heads to the poll on referendum day. ( ABC News: Natalie Whiting )

The deputy speaker of Bougainville's Parliament, Francesca Semoso, said she was emotional when she cast her vote last month.

"It's been a long time coming," she told the ABC. "I was a little girl as this was being talked about.

"We've lost people that have worked so hard.

The Bougainville Referendum Commission vote counting centre. ( ABC News: Natalie Whiting )

"For me personally, it's my father who's always been a strong supporter of peace … and supporter of making sure everyone in the community were able to have a voice."

Central to the conflict that led to the vote was Bougainville's rich resources. The autonomous region was once home to the world's largest open-cut copper mine at Panguna, which provided up to 45 per cent of PNG's export profits.

Many felt mining profits were not being shared fairly between PNG and Bougainville — or even between different landowner groups at the mine site — while pollution from the Panguna operation also created tension.

Bougainville sits in the same island chain as Solomon Islands, despite being part of PNG. ( ABC News: Jarrod Fankhauser )

The civil war that subsequently broke out between the Bougainville Revolutionary Army, Papua New Guinean forces and other pro-PNG militias in Bougainville saw the mine shut down in 1989.

The mine has remained closed despite controversial attempts to reopen it in recent years.

How the voting unfolded

A volunteer collecting votes from a patient and their carer at Buka hospital. ( Facebook: Bougainville Referendum Commission )

To ensure everyone enrolled had a chance to vote, referendum officials visited people in hospitals and police cells.

Voting was also made available to Bougainvilleans working on mine sites around PNG and those working in Australia and Solomon Islands.

Arrangements were made to allow young upe men to vote in the referendum. ( Bougainville Referendum Commission )

Special arrangements were made to allow upes — boys and young men undertaking their coming of age initiations — to vote in Bougainville's historic referendum.

The young men have to spend an extended period in isolation in the bush, where they learn traditional practices and are forbidden to be seen by women.

Bertie Ahearn watched the counting with Australia's high commissioner to PNG, Bruce Davis. ( ABC News: Natalie Whiting )

All or most of the voting was closely watched by several groups of observers, including a team of 11 sent by the Australian Government and led by the former Australian MP Jane Prentice, who has her own very personal connection to the region.

"My husband was involved in the peace arrangements and the conflict resolution. We had many of the key players come and stay with us in Brisbane," she told the ABC's Pacific Beat program earlier this month.

"For me, it was quite emotional.

"To see them back in their own village, to meet them and be part of what they see as the next step in their future was incredibly special."

What happens now?

Despite the outcome of the vote, the future of Bougainville is still uncertain.

PNG and Bougainville are now expected to hold negotiations and present an option for the PNG Parliament to vote on.

That process could take several years, and PNG's Minister for Bougainville, Sir Puka Temu, said his Government was firm in its desire to hold on to the island.

"We don't want any part of Papua New Guinea to break away," Sir Puka told Pacific Beat last month.

"We don't want to set a precedent for the other 21 provinces. That will be our firm position".