The Pacific Islands Forum (PIF) consists of 16 member countries, including Fiji which was recently reinstated following a successful elections this year.
But Fiji has refused to officially rejoin the Pacific Islands Forum unless Australia and New Zealand are excluded from the group.
It has launched an alternative regional bloc, the Pacific Islands Development Forum (PIDF), to further the interests of Pacific Island nations.
Mr O'Neill said that the structure of the Pacific Islands Forum does not need changing.
"We must make sure that we don't forget that we all live in the same region and Australia and New Zealand are very much part of that region," he said.
"We need to encourage more dialogue and more common sense to prevail in these discussions. Our traditional partners like Australia and New Zealand continue to be important to the Pacific Island countries; it is foolhardy to think this is not the case.
PNG prime minister Peter O'Neill
"We just had a review of the new Pacific Plan which was adopted by the leaders in Palau. We need to start implementing some of these strategies that we are putting in place rather than talking about creating a new structure that is going to be costly and duplication."
A meeting scheduled for February will bring together Australian and Pacific representatives in Sydney to review the make-up and responsibilities of the regional bodies.
Australia's Parliamentary Secretary for Foreign Affairs, Senator Brett Mason, said it was "a fair question to ask whether we can improve the regional architecture".
"Clearly the new plan for Pacific regionalism was updated to better focus the efforts of Pacific Island nations on a more cooperative approach to the challenges facing the region," he said.
"If we can improve that architecture that will be good for all Pacific Island nations.
"Is there room for improvement? Yes, of course there is."
Pacific nations seek to engage with Asian powers: O'Neill
Mr O'Neill also dismissed claims that Papua New Guinea is trying to assert regional leadership over Fiji.
"We are not vying to become the leader of the Pacific," he said.
"We are of course the biggest economy, we've got the biggest population and biggest country in the Pacific.
"So everything we do is big in size. Decisions we make are quite large in terms of its influence, so we don't see it as rivalry between the two countries."
Chinese president Xi Jinping and Indian prime minister Narendra Modi both recently visited Fiji and held talks with leaders from other Pacific countries including Papua New Guinea, Tonga, Samoa, Vanuatu, Micronesia, Cook Islands and Niue.
Mr O'Neill said Pacific nations can engage with the rising economic powers of Asia without neglecting its close ties with Australia and New Zealand.
"Our traditional partners like Australia and New Zealand continue to be important to the Pacific Island countries; it is foolhardy to think this is not the case because we live in the region, we understand each other, our people travel between our countries," he said.
"But Pacific countries also need to trade with the growing influence in Asia, to deal with India and China as the two biggest economies in that region.
"We need to stay engaged and in line with what we are trying to achieve in terms of making sure our people take advantage of the opportunities that are available to us."