The contentious West Papuan issue will not be formally discussed between Papua New Guinea and Indonesia during president Susilo Bambang Yudhoyono's two-day visit to Port Moresby.
Mr Yudhoyono arrived in PNG yesterday afternoon and met the Prime Minister, Sir Michael Somare.
However, the Port Moresby governor, Powes Parkop, is confident a petition calling for great Papuan autonomy will make it to Dr Yudhoyono.
Mr Parkop has told the AAP news agency that he has given the foreign minister, Sam Abal, the protest petition that calls for better treatment of Papuan people.
West Papua's plight has been a thorny political issue for the two countries as PNG has ethnic connections to the two million Melanesians who for the past 40 years have lived in Indonesia's poorest province.
PNG and Indonesia share a 750 kilometre land border and are expected to discuss climate change, the Coral Triangle Initiative and then sign agreements on defence co-operation and taxation.