Almost 98 percent of the 181,067 votes cast upheld independence in a historic poll that is part of a peace deal struck in 1998 after a decade-long war between Bougainville’s rebel fighters and the Papua New Guinea Defence Force (PNGDF).
"Around 85 percent of the total people on the referendum roll have cast their vote in an environment that was conducive to a free, fair and credible process," said the commission's chairman Bertie Ahern ahead of the result.
Voters in Bougainville had to choose between full independence and greater autonomy, just 3,043 voters backed the second option.
“There’s tears, tears of joy, raw emotion - people have waited a long time,” Referendum Chairman Bertie Ahern said in the town of Buka adding that “the pen is always mightier than the sword.”
Pajomile Minaka, from Bougainville’s southern region, told Reuters he was taking a law course to equip himself to help rebuild his homeland.
“That’s my dream, to go and rebuild,” said the 36-year old, who was a child during the conflict. “We need the best policies, the best laws, to be the best country. We are reborn.”
The comprehensive vote will serve to strengthen separatists as they start discussions on the terms of the independence with the Papua New Guinea government. Any agreement reached between both sides in the talks would still need to be ratified by Papua New Guinea's parliament.
French explorer Louis de Bougainville arrived on the archipelago in 1768 and since, control over the islands has been transferred from Germany to Australia to Japan to the United Nations and to Papua New Guinea.
Many Bougainvilleans feel culturally closer to the neighboring Solomon Islands, with a strong provincial identity, distinct from the tribal factions of other regions of Papua New Guinea.
The 1988-1998 conflict between Bougainville and Papua New Guinea originated in a struggle over revenues from the now-shuttered Panguna copper mine, which at the time accounted for more than 40 percent of Papua New Guinea's exports. The mine is estimated to still hold more than five million tonnes of copper and 19 million ounces of gold, worth billions of dollars at current market prices.