The South Pacific islands of Bougainville have overwhelmingly voted to be independent from Papua New Guinea, the referendum commission said on Wednesday, in a historic poll that will trigger separation negotiations between the two governments.

Almost 98 per cent of the 1,81,067 votes cast backed independence in the non-binding poll that is part of a peace pact struck in the aftermath of a decade-long war between Bougainville's rebel fighters and PNG forces, which ended in 1998.

The referendum gave voters in the island cluster a choice between independence and greater autonomy.

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